From dicknetherlands at gmail.com Sun Jan 4 07:01:21 2009 From: dicknetherlands at gmail.com (Richard Holland) Date: Sun, 4 Jan 2009 12:01:21 +0000 Subject: [Biojava-dev] Licenses Message-ID: Hi all, I know this has been asked before, but it has been pointed out again from our friends at the Debian project that licence declarations are missing from several source files in the BioJava subversion repository, particularly the bytecode packages. This prevents it from being packaged up as a Debian .deb file, as their requirements are that licence declarations appear in every single source file inside the file. It would be very useful if everyone who has ever contributed to BioJava could go and check their files and make sure they are licenced correctly (LGPL). I know that's a tall order, but we really do need to find everyone - even if you can't make the changes yourself, you do need to give me or someone else on this list permission to make the changes for you. cheers, Richard From simpleyrx at 163.com Fri Jan 9 01:02:24 2009 From: simpleyrx at 163.com (simpleyrx) Date: Fri, 9 Jan 2009 14:02:24 +0800 (CST) Subject: [Biojava-dev] a question on NeedlemanWunsch.java Message-ID: <20925918.184201231480944506.JavaMail.coremail@bj163app61.163.com> Dear experts In NeedlemanWunsch.java code , for (i = 1; i <= squery.length(); i++) for (j = 1; j <= ssubject.length(); j++) { E[i][j] = Math.min(E[i][j - 1], CostMatrix[i][j - 1] + insert) + gapExt; F[i][j] = Math.min(F[i - 1][j], CostMatrix[i - 1][j] + delete) + gapExt; CostMatrix[i][j] = min(E[i][j], F[i][j], CostMatrix[i - 1][j - 1] - matchReplace(squery, ssubject, i, j)); } In some papers , they used Math.max instead of Min. I wonder why ? -- Renxiang Yan From bugzilla-daemon at portal.open-bio.org Sun Jan 11 22:31:50 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sun, 11 Jan 2009 22:31:50 -0500 Subject: [Biojava-dev] [Bug 2536] GenBankFormat Doesn't Support Bond Features In-Reply-To: Message-ID: <200901120331.n0C3Voq9022652@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2536 ------- Comment #7 from james at carmanconsulting.com 2009-01-11 22:31 EST ------- Should this be included in the latest 1.6 release? I seem to be having the issue with the 1.6.1 version that I've downloaded. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From ola.spjuth at farmbio.uu.se Tue Jan 13 02:38:34 2009 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Tue, 13 Jan 2009 08:38:34 +0100 Subject: [Biojava-dev] XML Schema Message-ID: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> Hi, Does it exist an XML Schema (or compatible) for Biojava, or even better a common schema for the Bio* projects? If not, is this in the pipe for Biojava3? /Ola From markjschreiber at gmail.com Tue Jan 13 05:24:54 2009 From: markjschreiber at gmail.com (Mark Schreiber) Date: Tue, 13 Jan 2009 18:24:54 +0800 Subject: [Biojava-dev] XML Schema In-Reply-To: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> References: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> Message-ID: <93b45ca50901130224x3eb19fdm1dcbe3487c2aba21@mail.gmail.com> The plan for biojava3 is that most or all of it will be POJO enough to support JAXB binding. The JPA implementation of BioSQL objects in BJ3 is already XML compatible as the objects are entity beans and can be transported via JAX-RPC. - Mark On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth wrote: > > Hi, > > Does it exist an XML Schema (or compatible) for Biojava, or even better a common schema for the Bio* projects? If not, is this in the pipe for Biojava3? > > /Ola > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev From ola.spjuth at farmbio.uu.se Tue Jan 13 06:46:50 2009 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Tue, 13 Jan 2009 12:46:50 +0100 Subject: [Biojava-dev] XML Schema In-Reply-To: <93b45ca50901130224x3eb19fdm1dcbe3487c2aba21@mail.gmail.com> References: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> <93b45ca50901130224x3eb19fdm1dcbe3487c2aba21@mail.gmail.com> Message-ID: <38E3B89D-0672-49BC-85F2-C8D579CEA260@farmbio.uu.se> Hi Mark, Thanks for the quick answer. Never used JAXB myself; does this procedure support generation of an XML schema from code? I assume you will annotate the POJO's with JAXB metadata? I usually work the other way around and generate my model code from a model (usually based on an XML Schema), I guess in the end it boils down to the same result? Anyway, what is the preferred way of serializing current Biojava(X) objects to XML? Via BioSQL in some way? Cheers, /Ola On 13 jan 2009, at 11.24, Mark Schreiber wrote: > The plan for biojava3 is that most or all of it will be POJO enough to > support JAXB binding. The JPA implementation of BioSQL objects in BJ3 > is already XML compatible as the objects are entity beans and can be > transported via JAX-RPC. > > - Mark > > On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth > wrote: >> >> Hi, >> >> Does it exist an XML Schema (or compatible) for Biojava, or even >> better a common schema for the Bio* projects? If not, is this in >> the pipe for Biojava3? >> >> /Ola >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev From markjschreiber at gmail.com Tue Jan 13 07:52:38 2009 From: markjschreiber at gmail.com (Mark Schreiber) Date: Tue, 13 Jan 2009 20:52:38 +0800 Subject: [Biojava-dev] XML Schema In-Reply-To: <38E3B89D-0672-49BC-85F2-C8D579CEA260@farmbio.uu.se> References: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> <93b45ca50901130224x3eb19fdm1dcbe3487c2aba21@mail.gmail.com> <38E3B89D-0672-49BC-85F2-C8D579CEA260@farmbio.uu.se> Message-ID: <93b45ca50901130452w202b7828t87b6b03a5b2b59ad@mail.gmail.com> Hi - With JAXB you can annotate the POJOs with JAXB instructions although I believe if you have a beany object and no annotation you get default behavior if you don't annotate it. I think you can get a schema from an object or auto generate objects from a schema (unless it is a bit complex in which case you might need to put JAXB tags in the schema). There is no clearcut way to get from biojavax to XML. This is because of the heavy use of singletons and non-bean like objects in biojavax (something that BJ3 will hopefully get away from). If you want to make a custom XML serializer/ deserializer my recommendation would be to put in a middle (transport) layer of beans that operate like the DTO's of older EJB designs. They would basically be data holders that you can generate from biojavax objects and then send to XML. Going the other way you would generate these beans from XML and then use the beans to generate biojavax objects (with singletons etc). - Mark On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth wrote: > Hi Mark, > > Thanks for the quick answer. Never used JAXB myself; does this procedure > support generation of an XML schema from code? I assume you will annotate > the POJO's with JAXB metadata? I usually work the other way around and > generate my model code from a model (usually based on an XML Schema), I > guess in the end it boils down to the same result? > > Anyway, what is the preferred way of serializing current Biojava(X) objects > to XML? Via BioSQL in some way? > > Cheers, > > /Ola > > On 13 jan 2009, at 11.24, Mark Schreiber wrote: > >> The plan for biojava3 is that most or all of it will be POJO enough to >> support JAXB binding. The JPA implementation of BioSQL objects in BJ3 >> is already XML compatible as the objects are entity beans and can be >> transported via JAX-RPC. >> >> - Mark >> >> On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth >> wrote: >>> >>> Hi, >>> >>> Does it exist an XML Schema (or compatible) for Biojava, or even better a >>> common schema for the Bio* projects? If not, is this in the pipe for >>> Biojava3? >>> >>> /Ola >>> >>> _______________________________________________ >>> biojava-dev mailing list >>> biojava-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev > > From markjschreiber at gmail.com Tue Jan 13 07:54:10 2009 From: markjschreiber at gmail.com (Mark Schreiber) Date: Tue, 13 Jan 2009 20:54:10 +0800 Subject: [Biojava-dev] XML Schema In-Reply-To: <93b45ca50901130452w202b7828t87b6b03a5b2b59ad@mail.gmail.com> References: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> <93b45ca50901130224x3eb19fdm1dcbe3487c2aba21@mail.gmail.com> <38E3B89D-0672-49BC-85F2-C8D579CEA260@farmbio.uu.se> <93b45ca50901130452w202b7828t87b6b03a5b2b59ad@mail.gmail.com> Message-ID: <93b45ca50901130454r1d9aa223j5646897950389108@mail.gmail.com> Note that you could easily use the BJ3 BioSQL entity beans as the DTO layer for biojavax if you wanted to write methods to convert biojavax to the entity beans (shouldn't be hard as there is a very close relationship). - Mark On Tue, Jan 13, 2009 at 8:52 PM, Mark Schreiber wrote: > Hi - > > With JAXB you can annotate the POJOs with JAXB instructions although I > believe if you have a beany object and no annotation you get default > behavior if you don't annotate it. I think you can get a schema from > an object or auto generate objects from a schema (unless it is a bit > complex in which case you might need to put JAXB tags in the schema). > > There is no clearcut way to get from biojavax to XML. This is because > of the heavy use of singletons and non-bean like objects in biojavax > (something that BJ3 will hopefully get away from). If you want to make > a custom XML serializer/ deserializer my recommendation would be to > put in a middle (transport) layer of beans that operate like the DTO's > of older EJB designs. They would basically be data holders that you > can generate from biojavax objects and then send to XML. Going the > other way you would generate these beans from XML and then use the > beans to generate biojavax objects (with singletons etc). > > - Mark > > On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth wrote: >> Hi Mark, >> >> Thanks for the quick answer. Never used JAXB myself; does this procedure >> support generation of an XML schema from code? I assume you will annotate >> the POJO's with JAXB metadata? I usually work the other way around and >> generate my model code from a model (usually based on an XML Schema), I >> guess in the end it boils down to the same result? >> >> Anyway, what is the preferred way of serializing current Biojava(X) objects >> to XML? Via BioSQL in some way? >> >> Cheers, >> >> /Ola >> >> On 13 jan 2009, at 11.24, Mark Schreiber wrote: >> >>> The plan for biojava3 is that most or all of it will be POJO enough to >>> support JAXB binding. The JPA implementation of BioSQL objects in BJ3 >>> is already XML compatible as the objects are entity beans and can be >>> transported via JAX-RPC. >>> >>> - Mark >>> >>> On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth >>> wrote: >>>> >>>> Hi, >>>> >>>> Does it exist an XML Schema (or compatible) for Biojava, or even better a >>>> common schema for the Bio* projects? If not, is this in the pipe for >>>> Biojava3? >>>> >>>> /Ola >>>> >>>> _______________________________________________ >>>> biojava-dev mailing list >>>> biojava-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> >> > From ola.spjuth at farmbio.uu.se Tue Jan 13 08:47:53 2009 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Tue, 13 Jan 2009 14:47:53 +0100 Subject: [Biojava-dev] XML Schema In-Reply-To: <93b45ca50901130452w202b7828t87b6b03a5b2b59ad@mail.gmail.com> References: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> <93b45ca50901130224x3eb19fdm1dcbe3487c2aba21@mail.gmail.com> <38E3B89D-0672-49BC-85F2-C8D579CEA260@farmbio.uu.se> <93b45ca50901130452w202b7828t87b6b03a5b2b59ad@mail.gmail.com> Message-ID: Hi, Seems a bit too time-consuming for me for the moment, I'll have to wait for BJ3. Is there a roadmap/timeframe for this? I just want to suggest (for BJ3 development) to have/generate an XML Schema. At least I would benefit from this since I generate service bindings on the fly and also want to validate data in remote services. Cheers, /Ola On 13 jan 2009, at 13.52, Mark Schreiber wrote: > Hi - > > With JAXB you can annotate the POJOs with JAXB instructions although I > believe if you have a beany object and no annotation you get default > behavior if you don't annotate it. I think you can get a schema from > an object or auto generate objects from a schema (unless it is a bit > complex in which case you might need to put JAXB tags in the schema). > > There is no clearcut way to get from biojavax to XML. This is because > of the heavy use of singletons and non-bean like objects in biojavax > (something that BJ3 will hopefully get away from). If you want to make > a custom XML serializer/ deserializer my recommendation would be to > put in a middle (transport) layer of beans that operate like the DTO's > of older EJB designs. They would basically be data holders that you > can generate from biojavax objects and then send to XML. Going the > other way you would generate these beans from XML and then use the > beans to generate biojavax objects (with singletons etc). > > - Mark > > On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth > wrote: >> Hi Mark, >> >> Thanks for the quick answer. Never used JAXB myself; does this >> procedure >> support generation of an XML schema from code? I assume you will >> annotate >> the POJO's with JAXB metadata? I usually work the other way around >> and >> generate my model code from a model (usually based on an XML >> Schema), I >> guess in the end it boils down to the same result? >> >> Anyway, what is the preferred way of serializing current Biojava(X) >> objects >> to XML? Via BioSQL in some way? >> >> Cheers, >> >> /Ola >> >> On 13 jan 2009, at 11.24, Mark Schreiber wrote: >> >>> The plan for biojava3 is that most or all of it will be POJO >>> enough to >>> support JAXB binding. The JPA implementation of BioSQL objects in >>> BJ3 >>> is already XML compatible as the objects are entity beans and can be >>> transported via JAX-RPC. >>> >>> - Mark >>> >>> On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth >> > >>> wrote: >>>> >>>> Hi, >>>> >>>> Does it exist an XML Schema (or compatible) for Biojava, or even >>>> better a >>>> common schema for the Bio* projects? If not, is this in the pipe >>>> for >>>> Biojava3? >>>> >>>> /Ola >>>> >>>> _______________________________________________ >>>> biojava-dev mailing list >>>> biojava-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> >> From holland at eaglegenomics.com Tue Jan 13 08:47:42 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Tue, 13 Jan 2009 13:47:42 +0000 Subject: [Biojava-dev] XML Schema In-Reply-To: References: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> <93b45ca50901130224x3eb19fdm1dcbe3487c2aba21@mail.gmail.com> <38E3B89D-0672-49BC-85F2-C8D579CEA260@farmbio.uu.se> <93b45ca50901130452w202b7828t87b6b03a5b2b59ad@mail.gmail.com> Message-ID: <496C9B7E.2030600@eaglegenomics.com> Sorry about that last one. I understand what you're getting at now. There is no current roadmap/timeline for BJ3 as there is nobody developing it except me and I've got lots of other things to do at the moment, which involve getting paid and so sadly have to take priority. Maybe there is someone out there who is willing to take responsibility for it and project manage the BJ3 development? cheers, Richard Ola Spjuth wrote: > Hi, > > Seems a bit too time-consuming for me for the moment, I'll have to wait > for BJ3. Is there a roadmap/timeframe for this? > > I just want to suggest (for BJ3 development) to have/generate an XML > Schema. At least I would benefit from this since I generate service > bindings on the fly and also want to validate data in remote services. > > Cheers, > > /Ola > > On 13 jan 2009, at 13.52, Mark Schreiber wrote: > >> Hi - >> >> With JAXB you can annotate the POJOs with JAXB instructions although I >> believe if you have a beany object and no annotation you get default >> behavior if you don't annotate it. I think you can get a schema from >> an object or auto generate objects from a schema (unless it is a bit >> complex in which case you might need to put JAXB tags in the schema). >> >> There is no clearcut way to get from biojavax to XML. This is because >> of the heavy use of singletons and non-bean like objects in biojavax >> (something that BJ3 will hopefully get away from). If you want to make >> a custom XML serializer/ deserializer my recommendation would be to >> put in a middle (transport) layer of beans that operate like the DTO's >> of older EJB designs. They would basically be data holders that you >> can generate from biojavax objects and then send to XML. Going the >> other way you would generate these beans from XML and then use the >> beans to generate biojavax objects (with singletons etc). >> >> - Mark >> >> On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth >> wrote: >>> Hi Mark, >>> >>> Thanks for the quick answer. Never used JAXB myself; does this procedure >>> support generation of an XML schema from code? I assume you will >>> annotate >>> the POJO's with JAXB metadata? I usually work the other way around and >>> generate my model code from a model (usually based on an XML Schema), I >>> guess in the end it boils down to the same result? >>> >>> Anyway, what is the preferred way of serializing current Biojava(X) >>> objects >>> to XML? Via BioSQL in some way? >>> >>> Cheers, >>> >>> /Ola >>> >>> On 13 jan 2009, at 11.24, Mark Schreiber wrote: >>> >>>> The plan for biojava3 is that most or all of it will be POJO enough to >>>> support JAXB binding. The JPA implementation of BioSQL objects in BJ3 >>>> is already XML compatible as the objects are entity beans and can be >>>> transported via JAX-RPC. >>>> >>>> - Mark >>>> >>>> On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth >>>> wrote: >>>>> >>>>> Hi, >>>>> >>>>> Does it exist an XML Schema (or compatible) for Biojava, or even >>>>> better a >>>>> common schema for the Bio* projects? If not, is this in the pipe for >>>>> Biojava3? >>>>> >>>>> /Ola >>>>> >>>>> _______________________________________________ >>>>> biojava-dev mailing list >>>>> biojava-dev at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>> >>> > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From markjschreiber at gmail.com Tue Jan 13 09:03:26 2009 From: markjschreiber at gmail.com (markjschreiber at gmail.com) Date: Tue, 13 Jan 2009 14:03:26 +0000 Subject: [Biojava-dev] XML Schema Message-ID: <00163646ccdeea728e04605dafcc@google.com> It would probably be less time consuming to write the bridge than wait for BJ3 which has no time frame as yet. I also don't think there will be (or should be) a unified XML schema for BJ3 as it will be much more modular (by design). Possibly each module could have a schema if relevant. Generally it is hoped that each module will be compatible with bean like design (unless there is a good reason not to) so this would implicitly mean there will be simple XML schema generation. - Mark On Jan 13, 2009 9:47pm, Ola Spjuth wrote: > Hi, > > > > Seems a bit too time-consuming for me for the moment, I'll have to wait for BJ3. Is there a roadmap/timeframe for this? > > > > I just want to suggest (for BJ3 development) to have/generate an XML Schema. At least I would benefit from this since I generate service bindings on the fly and also want to validate data in remote services. > > > > Cheers, > > > > /Ola > > > > On 13 jan 2009, at 13.52, Mark Schreiber wrote: > > > > > Hi - > > > > With JAXB you can annotate the POJOs with JAXB instructions although I > > believe if you have a beany object and no annotation you get default > > behavior if you don't annotate it. I think you can get a schema from > > an object or auto generate objects from a schema (unless it is a bit > > complex in which case you might need to put JAXB tags in the schema). > > > > There is no clearcut way to get from biojavax to XML. This is because > > of the heavy use of singletons and non-bean like objects in biojavax > > (something that BJ3 will hopefully get away from). If you want to make > > a custom XML serializer/ deserializer my recommendation would be to > > put in a middle (transport) layer of beans that operate like the DTO's > > of older EJB designs. They would basically be data holders that you > > can generate from biojavax objects and then send to XML. Going the > > other way you would generate these beans from XML and then use the > > beans to generate biojavax objects (with singletons etc). > > > > - Mark > > > > On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth ola.spjuth at farmbio.uu.se> wrote: > > > Hi Mark, > > > > Thanks for the quick answer. Never used JAXB myself; does this procedure > > support generation of an XML schema from code? I assume you will annotate > > the POJO's with JAXB metadata? I usually work the other way around and > > generate my model code from a model (usually based on an XML Schema), I > > guess in the end it boils down to the same result? > > > > Anyway, what is the preferred way of serializing current Biojava(X) objects > > to XML? Via BioSQL in some way? > > > > Cheers, > > > > /Ola > > > > On 13 jan 2009, at 11.24, Mark Schreiber wrote: > > > > > The plan for biojava3 is that most or all of it will be POJO enough to > > support JAXB binding. The JPA implementation of BioSQL objects in BJ3 > > is already XML compatible as the objects are entity beans and can be > > transported via JAX-RPC. > > > > - Mark > > > > On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth ola.spjuth at farmbio.uu.se> > > wrote: > > > > > Hi, > > > > Does it exist an XML Schema (or compatible) for Biojava, or even better a > > common schema for the Bio* projects? If not, is this in the pipe for > > Biojava3? > > > > /Ola > > > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > > > > > > > > From holland at eaglegenomics.com Tue Jan 13 08:15:51 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Tue, 13 Jan 2009 13:15:51 +0000 Subject: [Biojava-dev] XML Schema In-Reply-To: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> References: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> Message-ID: <496C9407.4090401@eaglegenomics.com> I don't understand your request. XML Schemas are for describing XML documents. BioJava is not an XML document, it is a piece of Java software! cheers, Richard Ola Spjuth wrote: > Hi, > > Does it exist an XML Schema (or compatible) for Biojava, or even better > a common schema for the Bio* projects? If not, is this in the pipe for > Biojava3? > > /Ola > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From TSN at atp.dk Tue Jan 13 09:24:31 2009 From: TSN at atp.dk (TSN at atp.dk) Date: Tue, 13 Jan 2009 15:24:31 +0100 Subject: [Biojava-dev] Vedr.: biojava-dev Digest, Vol 70, Issue 2 In-Reply-To: Message-ID: Hello ! Regarding XML-Schemas - Have You ever tried to use XML-beans. As a proffesional JAVA developer I have had some very good experiences in converting between JAVA objects and complex XML structures with XML-beans. You have to setup a system for generating the beans, but afterwards the benefir is worth it /Tom Stevns - DK biojava-dev-request at lists.open-bio.org Sendt af: biojava-dev-bounces at lists.open-bio.org 13-01-2009 15:03 Besvar venligst til biojava-dev at lists.open-bio.org Til biojava-dev at lists.open-bio.org cc Emne biojava-dev Digest, Vol 70, Issue 2 Send biojava-dev mailing list submissions to biojava-dev at lists.open-bio.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.open-bio.org/mailman/listinfo/biojava-dev or, via email, send a message with subject or body 'help' to biojava-dev-request at lists.open-bio.org You can reach the person managing the list at biojava-dev-owner at lists.open-bio.org When replying, please edit your Subject line so it is more specific than "Re: Contents of biojava-dev digest..." Today's Topics: 1. Re: XML Schema (Mark Schreiber) 2. Re: XML Schema (Ola Spjuth) 3. Re: XML Schema (Mark Schreiber) 4. Re: XML Schema (Mark Schreiber) 5. Re: XML Schema (Ola Spjuth) 6. Re: XML Schema (Richard Holland) 7. Re: XML Schema (markjschreiber at gmail.com) ---------------------------------------------------------------------- Message: 1 Date: Tue, 13 Jan 2009 18:24:54 +0800 From: "Mark Schreiber" Subject: Re: [Biojava-dev] XML Schema To: "Ola Spjuth" Cc: biojava-dev at biojava.org Message-ID: <93b45ca50901130224x3eb19fdm1dcbe3487c2aba21 at mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 The plan for biojava3 is that most or all of it will be POJO enough to support JAXB binding. The JPA implementation of BioSQL objects in BJ3 is already XML compatible as the objects are entity beans and can be transported via JAX-RPC. - Mark On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth wrote: > > Hi, > > Does it exist an XML Schema (or compatible) for Biojava, or even better a common schema for the Bio* projects? If not, is this in the pipe for Biojava3? > > /Ola > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev ------------------------------ Message: 2 Date: Tue, 13 Jan 2009 12:46:50 +0100 From: Ola Spjuth Subject: Re: [Biojava-dev] XML Schema To: Mark Schreiber Cc: biojava-dev at biojava.org Message-ID: <38E3B89D-0672-49BC-85F2-C8D579CEA260 at farmbio.uu.se> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Hi Mark, Thanks for the quick answer. Never used JAXB myself; does this procedure support generation of an XML schema from code? I assume you will annotate the POJO's with JAXB metadata? I usually work the other way around and generate my model code from a model (usually based on an XML Schema), I guess in the end it boils down to the same result? Anyway, what is the preferred way of serializing current Biojava(X) objects to XML? Via BioSQL in some way? Cheers, /Ola On 13 jan 2009, at 11.24, Mark Schreiber wrote: > The plan for biojava3 is that most or all of it will be POJO enough to > support JAXB binding. The JPA implementation of BioSQL objects in BJ3 > is already XML compatible as the objects are entity beans and can be > transported via JAX-RPC. > > - Mark > > On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth > wrote: >> >> Hi, >> >> Does it exist an XML Schema (or compatible) for Biojava, or even >> better a common schema for the Bio* projects? If not, is this in >> the pipe for Biojava3? >> >> /Ola >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev ------------------------------ Message: 3 Date: Tue, 13 Jan 2009 20:52:38 +0800 From: "Mark Schreiber" Subject: Re: [Biojava-dev] XML Schema To: "Ola Spjuth" Cc: biojava-dev at biojava.org Message-ID: <93b45ca50901130452w202b7828t87b6b03a5b2b59ad at mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi - With JAXB you can annotate the POJOs with JAXB instructions although I believe if you have a beany object and no annotation you get default behavior if you don't annotate it. I think you can get a schema from an object or auto generate objects from a schema (unless it is a bit complex in which case you might need to put JAXB tags in the schema). There is no clearcut way to get from biojavax to XML. This is because of the heavy use of singletons and non-bean like objects in biojavax (something that BJ3 will hopefully get away from). If you want to make a custom XML serializer/ deserializer my recommendation would be to put in a middle (transport) layer of beans that operate like the DTO's of older EJB designs. They would basically be data holders that you can generate from biojavax objects and then send to XML. Going the other way you would generate these beans from XML and then use the beans to generate biojavax objects (with singletons etc). - Mark On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth wrote: > Hi Mark, > > Thanks for the quick answer. Never used JAXB myself; does this procedure > support generation of an XML schema from code? I assume you will annotate > the POJO's with JAXB metadata? I usually work the other way around and > generate my model code from a model (usually based on an XML Schema), I > guess in the end it boils down to the same result? > > Anyway, what is the preferred way of serializing current Biojava(X) objects > to XML? Via BioSQL in some way? > > Cheers, > > /Ola > > On 13 jan 2009, at 11.24, Mark Schreiber wrote: > >> The plan for biojava3 is that most or all of it will be POJO enough to >> support JAXB binding. The JPA implementation of BioSQL objects in BJ3 >> is already XML compatible as the objects are entity beans and can be >> transported via JAX-RPC. >> >> - Mark >> >> On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth >> wrote: >>> >>> Hi, >>> >>> Does it exist an XML Schema (or compatible) for Biojava, or even better a >>> common schema for the Bio* projects? If not, is this in the pipe for >>> Biojava3? >>> >>> /Ola >>> >>> _______________________________________________ >>> biojava-dev mailing list >>> biojava-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev > > ------------------------------ Message: 4 Date: Tue, 13 Jan 2009 20:54:10 +0800 From: "Mark Schreiber" Subject: Re: [Biojava-dev] XML Schema To: "Ola Spjuth" Cc: biojava-dev at biojava.org Message-ID: <93b45ca50901130454r1d9aa223j5646897950389108 at mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Note that you could easily use the BJ3 BioSQL entity beans as the DTO layer for biojavax if you wanted to write methods to convert biojavax to the entity beans (shouldn't be hard as there is a very close relationship). - Mark On Tue, Jan 13, 2009 at 8:52 PM, Mark Schreiber wrote: > Hi - > > With JAXB you can annotate the POJOs with JAXB instructions although I > believe if you have a beany object and no annotation you get default > behavior if you don't annotate it. I think you can get a schema from > an object or auto generate objects from a schema (unless it is a bit > complex in which case you might need to put JAXB tags in the schema). > > There is no clearcut way to get from biojavax to XML. This is because > of the heavy use of singletons and non-bean like objects in biojavax > (something that BJ3 will hopefully get away from). If you want to make > a custom XML serializer/ deserializer my recommendation would be to > put in a middle (transport) layer of beans that operate like the DTO's > of older EJB designs. They would basically be data holders that you > can generate from biojavax objects and then send to XML. Going the > other way you would generate these beans from XML and then use the > beans to generate biojavax objects (with singletons etc). > > - Mark > > On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth wrote: >> Hi Mark, >> >> Thanks for the quick answer. Never used JAXB myself; does this procedure >> support generation of an XML schema from code? I assume you will annotate >> the POJO's with JAXB metadata? I usually work the other way around and >> generate my model code from a model (usually based on an XML Schema), I >> guess in the end it boils down to the same result? >> >> Anyway, what is the preferred way of serializing current Biojava(X) objects >> to XML? Via BioSQL in some way? >> >> Cheers, >> >> /Ola >> >> On 13 jan 2009, at 11.24, Mark Schreiber wrote: >> >>> The plan for biojava3 is that most or all of it will be POJO enough to >>> support JAXB binding. The JPA implementation of BioSQL objects in BJ3 >>> is already XML compatible as the objects are entity beans and can be >>> transported via JAX-RPC. >>> >>> - Mark >>> >>> On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth >>> wrote: >>>> >>>> Hi, >>>> >>>> Does it exist an XML Schema (or compatible) for Biojava, or even better a >>>> common schema for the Bio* projects? If not, is this in the pipe for >>>> Biojava3? >>>> >>>> /Ola >>>> >>>> _______________________________________________ >>>> biojava-dev mailing list >>>> biojava-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> >> > ------------------------------ Message: 5 Date: Tue, 13 Jan 2009 14:47:53 +0100 From: Ola Spjuth Subject: Re: [Biojava-dev] XML Schema To: Mark Schreiber Cc: biojava-dev at biojava.org Message-ID: Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Hi, Seems a bit too time-consuming for me for the moment, I'll have to wait for BJ3. Is there a roadmap/timeframe for this? I just want to suggest (for BJ3 development) to have/generate an XML Schema. At least I would benefit from this since I generate service bindings on the fly and also want to validate data in remote services. Cheers, /Ola On 13 jan 2009, at 13.52, Mark Schreiber wrote: > Hi - > > With JAXB you can annotate the POJOs with JAXB instructions although I > believe if you have a beany object and no annotation you get default > behavior if you don't annotate it. I think you can get a schema from > an object or auto generate objects from a schema (unless it is a bit > complex in which case you might need to put JAXB tags in the schema). > > There is no clearcut way to get from biojavax to XML. This is because > of the heavy use of singletons and non-bean like objects in biojavax > (something that BJ3 will hopefully get away from). If you want to make > a custom XML serializer/ deserializer my recommendation would be to > put in a middle (transport) layer of beans that operate like the DTO's > of older EJB designs. They would basically be data holders that you > can generate from biojavax objects and then send to XML. Going the > other way you would generate these beans from XML and then use the > beans to generate biojavax objects (with singletons etc). > > - Mark > > On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth > wrote: >> Hi Mark, >> >> Thanks for the quick answer. Never used JAXB myself; does this >> procedure >> support generation of an XML schema from code? I assume you will >> annotate >> the POJO's with JAXB metadata? I usually work the other way around >> and >> generate my model code from a model (usually based on an XML >> Schema), I >> guess in the end it boils down to the same result? >> >> Anyway, what is the preferred way of serializing current Biojava(X) >> objects >> to XML? Via BioSQL in some way? >> >> Cheers, >> >> /Ola >> >> On 13 jan 2009, at 11.24, Mark Schreiber wrote: >> >>> The plan for biojava3 is that most or all of it will be POJO >>> enough to >>> support JAXB binding. The JPA implementation of BioSQL objects in >>> BJ3 >>> is already XML compatible as the objects are entity beans and can be >>> transported via JAX-RPC. >>> >>> - Mark >>> >>> On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth >> > >>> wrote: >>>> >>>> Hi, >>>> >>>> Does it exist an XML Schema (or compatible) for Biojava, or even >>>> better a >>>> common schema for the Bio* projects? If not, is this in the pipe >>>> for >>>> Biojava3? >>>> >>>> /Ola >>>> >>>> _______________________________________________ >>>> biojava-dev mailing list >>>> biojava-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> >> ------------------------------ Message: 6 Date: Tue, 13 Jan 2009 13:47:42 +0000 From: Richard Holland Subject: Re: [Biojava-dev] XML Schema To: Ola Spjuth Cc: biojava-dev at biojava.org Message-ID: <496C9B7E.2030600 at eaglegenomics.com> Content-Type: text/plain; charset=ISO-8859-1 Sorry about that last one. I understand what you're getting at now. There is no current roadmap/timeline for BJ3 as there is nobody developing it except me and I've got lots of other things to do at the moment, which involve getting paid and so sadly have to take priority. Maybe there is someone out there who is willing to take responsibility for it and project manage the BJ3 development? cheers, Richard Ola Spjuth wrote: > Hi, > > Seems a bit too time-consuming for me for the moment, I'll have to wait > for BJ3. Is there a roadmap/timeframe for this? > > I just want to suggest (for BJ3 development) to have/generate an XML > Schema. At least I would benefit from this since I generate service > bindings on the fly and also want to validate data in remote services. > > Cheers, > > /Ola > > On 13 jan 2009, at 13.52, Mark Schreiber wrote: > >> Hi - >> >> With JAXB you can annotate the POJOs with JAXB instructions although I >> believe if you have a beany object and no annotation you get default >> behavior if you don't annotate it. I think you can get a schema from >> an object or auto generate objects from a schema (unless it is a bit >> complex in which case you might need to put JAXB tags in the schema). >> >> There is no clearcut way to get from biojavax to XML. This is because >> of the heavy use of singletons and non-bean like objects in biojavax >> (something that BJ3 will hopefully get away from). If you want to make >> a custom XML serializer/ deserializer my recommendation would be to >> put in a middle (transport) layer of beans that operate like the DTO's >> of older EJB designs. They would basically be data holders that you >> can generate from biojavax objects and then send to XML. Going the >> other way you would generate these beans from XML and then use the >> beans to generate biojavax objects (with singletons etc). >> >> - Mark >> >> On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth >> wrote: >>> Hi Mark, >>> >>> Thanks for the quick answer. Never used JAXB myself; does this procedure >>> support generation of an XML schema from code? I assume you will >>> annotate >>> the POJO's with JAXB metadata? I usually work the other way around and >>> generate my model code from a model (usually based on an XML Schema), I >>> guess in the end it boils down to the same result? >>> >>> Anyway, what is the preferred way of serializing current Biojava(X) >>> objects >>> to XML? Via BioSQL in some way? >>> >>> Cheers, >>> >>> /Ola >>> >>> On 13 jan 2009, at 11.24, Mark Schreiber wrote: >>> >>>> The plan for biojava3 is that most or all of it will be POJO enough to >>>> support JAXB binding. The JPA implementation of BioSQL objects in BJ3 >>>> is already XML compatible as the objects are entity beans and can be >>>> transported via JAX-RPC. >>>> >>>> - Mark >>>> >>>> On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth >>>> wrote: >>>>> >>>>> Hi, >>>>> >>>>> Does it exist an XML Schema (or compatible) for Biojava, or even >>>>> better a >>>>> common schema for the Bio* projects? If not, is this in the pipe for >>>>> Biojava3? >>>>> >>>>> /Ola >>>>> >>>>> _______________________________________________ >>>>> biojava-dev mailing list >>>>> biojava-dev at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>> >>> > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ ------------------------------ Message: 7 Date: Tue, 13 Jan 2009 14:03:26 +0000 From: markjschreiber at gmail.com Subject: Re: [Biojava-dev] XML Schema To: Ola Spjuth , Mark Schreiber , biojava-dev at biojava.org Message-ID: <00163646ccdeea728e04605dafcc at google.com> Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes It would probably be less time consuming to write the bridge than wait for BJ3 which has no time frame as yet. I also don't think there will be (or should be) a unified XML schema for BJ3 as it will be much more modular (by design). Possibly each module could have a schema if relevant. Generally it is hoped that each module will be compatible with bean like design (unless there is a good reason not to) so this would implicitly mean there will be simple XML schema generation. - Mark On Jan 13, 2009 9:47pm, Ola Spjuth wrote: > Hi, > > > > Seems a bit too time-consuming for me for the moment, I'll have to wait for BJ3. Is there a roadmap/timeframe for this? > > > > I just want to suggest (for BJ3 development) to have/generate an XML Schema. At least I would benefit from this since I generate service bindings on the fly and also want to validate data in remote services. > > > > Cheers, > > > > /Ola > > > > On 13 jan 2009, at 13.52, Mark Schreiber wrote: > > > > > Hi - > > > > With JAXB you can annotate the POJOs with JAXB instructions although I > > believe if you have a beany object and no annotation you get default > > behavior if you don't annotate it. I think you can get a schema from > > an object or auto generate objects from a schema (unless it is a bit > > complex in which case you might need to put JAXB tags in the schema). > > > > There is no clearcut way to get from biojavax to XML. This is because > > of the heavy use of singletons and non-bean like objects in biojavax > > (something that BJ3 will hopefully get away from). If you want to make > > a custom XML serializer/ deserializer my recommendation would be to > > put in a middle (transport) layer of beans that operate like the DTO's > > of older EJB designs. They would basically be data holders that you > > can generate from biojavax objects and then send to XML. Going the > > other way you would generate these beans from XML and then use the > > beans to generate biojavax objects (with singletons etc). > > > > - Mark > > > > On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth ola.spjuth at farmbio.uu.se> wrote: > > > Hi Mark, > > > > Thanks for the quick answer. Never used JAXB myself; does this procedure > > support generation of an XML schema from code? I assume you will annotate > > the POJO's with JAXB metadata? I usually work the other way around and > > generate my model code from a model (usually based on an XML Schema), I > > guess in the end it boils down to the same result? > > > > Anyway, what is the preferred way of serializing current Biojava(X) objects > > to XML? Via BioSQL in some way? > > > > Cheers, > > > > /Ola > > > > On 13 jan 2009, at 11.24, Mark Schreiber wrote: > > > > > The plan for biojava3 is that most or all of it will be POJO enough to > > support JAXB binding. The JPA implementation of BioSQL objects in BJ3 > > is already XML compatible as the objects are entity beans and can be > > transported via JAX-RPC. > > > > - Mark > > > > On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth ola.spjuth at farmbio.uu.se> > > wrote: > > > > > Hi, > > > > Does it exist an XML Schema (or compatible) for Biojava, or even better a > > common schema for the Bio* projects? If not, is this in the pipe for > > Biojava3? > > > > /Ola > > > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > > > > > > > > ------------------------------ _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev End of biojava-dev Digest, Vol 70, Issue 2 ****************************************** From james at carmanconsulting.com Thu Jan 15 07:06:33 2009 From: james at carmanconsulting.com (James Carman) Date: Thu, 15 Jan 2009 07:06:33 -0500 Subject: [Biojava-dev] Bug 2536... Message-ID: The patch I supplied was supposed to be applied for bug: http://bugzilla.open-bio.org/show_bug.cgi?id=2536 However, I have downloaded the latest 1.6.1 release and it looks like I'm still having the same issues. Was the patch not applied to that branch or something? James From andreas at sdsc.edu Thu Jan 15 08:50:36 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 15 Jan 2009 14:50:36 +0100 Subject: [Biojava-dev] Bug 2536... In-Reply-To: References: Message-ID: <59a41c430901150550m75a772c3ueb51934cbaccb092@mail.gmail.com> Hi James, I applied your patch on July 4th 2008 (revision 4825). The 1.6 release was branched before that date. As such your patch is available via a recent SVN checkout and will become part of the next biojava 1.7. We don't have a release plan for that yet, but traditionally we do a release at some point before ISMB in late spring/early summer. Andreas On Thu, Jan 15, 2009 at 1:06 PM, James Carman wrote: > The patch I supplied was supposed to be applied for bug: > > http://bugzilla.open-bio.org/show_bug.cgi?id=2536 > > However, I have downloaded the latest 1.6.1 release and it looks like > I'm still having the same issues. Was the patch not applied to that > branch or something? > > James > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From james at carmanconsulting.com Thu Jan 15 09:30:22 2009 From: james at carmanconsulting.com (James Carman) Date: Thu, 15 Jan 2009 09:30:22 -0500 Subject: [Biojava-dev] Bug 2536... In-Reply-To: <59a41c430901150546v516208b5k203ba3cab2169eb1@mail.gmail.com> References: <59a41c430901150546v516208b5k203ba3cab2169eb1@mail.gmail.com> Message-ID: Ok, great. I guess we'll just do an internal 1.7 release, then. Thanks for the info! On Thu, Jan 15, 2009 at 8:46 AM, Andreas Prlic wrote: > Hi James, > > I applied your patch on July 4th 2008 (revision 4825). The 1.6 release > was branched before that date. As such your patch is available via a > recent SVN checkout and will become part of the next biojava 1.7. We > don't have a release plan for that yet, but traditionally we do a > release at some point before ISMB in late spring/early summer. > > Andreas > > On Thu, Jan 15, 2009 at 1:06 PM, James Carman > wrote: >> The patch I supplied was supposed to be applied for bug: >> >> http://bugzilla.open-bio.org/show_bug.cgi?id=2536 >> >> However, I have downloaded the latest 1.6.1 release and it looks like >> I'm still having the same issues. Was the patch not applied to that >> branch or something? >> >> James >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > From andreas at sdsc.edu Thu Jan 15 09:41:40 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 15 Jan 2009 15:41:40 +0100 Subject: [Biojava-dev] Bug 2536... In-Reply-To: References: <59a41c430901150546v516208b5k203ba3cab2169eb1@mail.gmail.com> Message-ID: <59a41c430901150641w3d7695c1kfa84e6321f924a45@mail.gmail.com> as usually you can also download a biojava.jar that is based on the latest build from http://www.spice-3d.org/cruise/ A On Thu, Jan 15, 2009 at 3:30 PM, James Carman wrote: > Ok, great. I guess we'll just do an internal 1.7 release, then. > Thanks for the info! > > On Thu, Jan 15, 2009 at 8:46 AM, Andreas Prlic wrote: >> Hi James, >> >> I applied your patch on July 4th 2008 (revision 4825). The 1.6 release >> was branched before that date. As such your patch is available via a >> recent SVN checkout and will become part of the next biojava 1.7. We >> don't have a release plan for that yet, but traditionally we do a >> release at some point before ISMB in late spring/early summer. >> >> Andreas >> >> On Thu, Jan 15, 2009 at 1:06 PM, James Carman >> wrote: >>> The patch I supplied was supposed to be applied for bug: >>> >>> http://bugzilla.open-bio.org/show_bug.cgi?id=2536 >>> >>> However, I have downloaded the latest 1.6.1 release and it looks like >>> I'm still having the same issues. Was the patch not applied to that >>> branch or something? >>> >>> James >>> _______________________________________________ >>> biojava-dev mailing list >>> biojava-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>> >> > From james at carmanconsulting.com Thu Jan 15 09:43:33 2009 From: james at carmanconsulting.com (James Carman) Date: Thu, 15 Jan 2009 09:43:33 -0500 Subject: [Biojava-dev] Bug 2536... In-Reply-To: <59a41c430901150641w3d7695c1kfa84e6321f924a45@mail.gmail.com> References: <59a41c430901150546v516208b5k203ba3cab2169eb1@mail.gmail.com> <59a41c430901150641w3d7695c1kfa84e6321f924a45@mail.gmail.com> Message-ID: Even better! Thanks, Andreas! On Thu, Jan 15, 2009 at 9:41 AM, Andreas Prlic wrote: > as usually you can also download a biojava.jar that is based on the > latest build from > http://www.spice-3d.org/cruise/ > > A > > On Thu, Jan 15, 2009 at 3:30 PM, James Carman > wrote: >> Ok, great. I guess we'll just do an internal 1.7 release, then. >> Thanks for the info! >> >> On Thu, Jan 15, 2009 at 8:46 AM, Andreas Prlic wrote: >>> Hi James, >>> >>> I applied your patch on July 4th 2008 (revision 4825). The 1.6 release >>> was branched before that date. As such your patch is available via a >>> recent SVN checkout and will become part of the next biojava 1.7. We >>> don't have a release plan for that yet, but traditionally we do a >>> release at some point before ISMB in late spring/early summer. >>> >>> Andreas >>> >>> On Thu, Jan 15, 2009 at 1:06 PM, James Carman >>> wrote: >>>> The patch I supplied was supposed to be applied for bug: >>>> >>>> http://bugzilla.open-bio.org/show_bug.cgi?id=2536 >>>> >>>> However, I have downloaded the latest 1.6.1 release and it looks like >>>> I'm still having the same issues. Was the patch not applied to that >>>> branch or something? >>>> >>>> James >>>> _______________________________________________ >>>> biojava-dev mailing list >>>> biojava-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>>> >>> >> > From bugzilla-daemon at portal.open-bio.org Fri Jan 23 08:45:19 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 23 Jan 2009 08:45:19 -0500 Subject: [Biojava-dev] [Bug 2741] New: oboFileParser - findUnescaped Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2741 Summary: oboFileParser - findUnescaped Product: BioJava Version: live (CVS source) Platform: PC OS/Version: Windows XP Status: NEW Severity: normal Priority: P2 Component: ontology AssignedTo: biojava-dev at biojava.org ReportedBy: alex.gawronski at gmail.com When the oboFileParser parser checks for quotes using findUnescaped, it never starts reading again. If there is a quote character then it ignores all the characters until it sees another quote character. The problem is that it never started reading again after it sees the second quote character. This caused the method to miss the escape character. I added "inQuotes = false;" to the findUnescaped method and it works fine. public static int findUnescaped(String str, char toChar, int startindex, int endindex, boolean honorQuotes) { boolean inQuotes = false; char quoteChar = '\0'; for (int i = startindex; i < endindex; i++) { char c = str.charAt(i); if (c == '\\') { i++; continue; } else if (inQuotes) { if (c == quoteChar) inQuotes = false; continue; } else if (c == toChar) { return i; } else if (honorQuotes && isQuote(c)) { inQuotes = true; quoteChar = c; } } return -1; } -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Jan 23 13:03:31 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 23 Jan 2009 13:03:31 -0500 Subject: [Biojava-dev] [Bug 2741] oboFileParser - findUnescaped In-Reply-To: Message-ID: <200901231803.n0NI3VRQ022333@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2741 ap3 at sanger.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #1 from ap3 at sanger.ac.uk 2009-01-23 13:03 EST ------- thanks for the patch, committed it to svn, Andreas -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From andreas at sdsc.edu Thu Jan 29 16:11:51 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 29 Jan 2009 13:11:51 -0800 Subject: [Biojava-dev] [Biojava-l] Problem with blast file parser In-Reply-To: <498217B3.4010703@Gmail.com> References: <497913F9.70009@Gmail.com> <4979ED9C.6040207@imbusch.net> <498217B3.4010703@Gmail.com> Message-ID: <59a41c430901291311w642a98am68b33cc6c78b15f1@mail.gmail.com> Hi, We had a couple of bug reports recently regarding issues that already got fixed in the latest biojava builds from SVN. I think it is time to start preparing the next biojava release ( 1.7 ) to make sure everybody gets up to the latest status... Andreas On Thu, Jan 29, 2009 at 12:55 PM, Marcel Huntemann wrote: > Hi Charles! > > I've "found" a solution now. After dealing a couple of days with the > terrible xml output of blast and BioJava's BlastXMLParser (which also > wasn't working properly), I decided to have a look at the source code and > try to figure out myself what was wrong with the BlastLikeSAXParser. So I > checked out the present status of the source code via the anonymous svn > checkout (howto here: http://biojava.org/wiki/CVS_to_SVN_Migration). After > a couple of hours and me not finding an error that could cause this > behavior, I thought I'll just give it a try and compiled the checked out > source via ant. Then used the new created biojava.jar and suddenly > everything went perfectly! > So, whatever the error was (unfortunately I don't have the old source code > to make a diff on certain files), it is already corrected in the > up-to-the-minute version in the subversion system. > Try it out! > > Cheers, > Marcel > > > Charles Imbusch wrote: >> Hello Marcel, >> >> I also do experience the problem that the parser is skipping >> the even result numbers. I have not found a sufficient solution >> for that, so I gave up on parsing on a blast result file containing >> multiple results. Instead I splitted up the big fasta file into >> serveral ones, so that I just get one result for one fasta file. >> That works, even it's not the best solution for it. >> >> Let me know if you find another solution for that problem. >> >> Cheers, >> Charles >> >> > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From dicknetherlands at gmail.com Sun Jan 4 12:01:21 2009 From: dicknetherlands at gmail.com (Richard Holland) Date: Sun, 4 Jan 2009 12:01:21 +0000 Subject: [Biojava-dev] Licenses Message-ID: Hi all, I know this has been asked before, but it has been pointed out again from our friends at the Debian project that licence declarations are missing from several source files in the BioJava subversion repository, particularly the bytecode packages. This prevents it from being packaged up as a Debian .deb file, as their requirements are that licence declarations appear in every single source file inside the file. It would be very useful if everyone who has ever contributed to BioJava could go and check their files and make sure they are licenced correctly (LGPL). I know that's a tall order, but we really do need to find everyone - even if you can't make the changes yourself, you do need to give me or someone else on this list permission to make the changes for you. cheers, Richard From simpleyrx at 163.com Fri Jan 9 06:02:24 2009 From: simpleyrx at 163.com (simpleyrx) Date: Fri, 9 Jan 2009 14:02:24 +0800 (CST) Subject: [Biojava-dev] a question on NeedlemanWunsch.java Message-ID: <20925918.184201231480944506.JavaMail.coremail@bj163app61.163.com> Dear experts In NeedlemanWunsch.java code , for (i = 1; i <= squery.length(); i++) for (j = 1; j <= ssubject.length(); j++) { E[i][j] = Math.min(E[i][j - 1], CostMatrix[i][j - 1] + insert) + gapExt; F[i][j] = Math.min(F[i - 1][j], CostMatrix[i - 1][j] + delete) + gapExt; CostMatrix[i][j] = min(E[i][j], F[i][j], CostMatrix[i - 1][j - 1] - matchReplace(squery, ssubject, i, j)); } In some papers , they used Math.max instead of Min. I wonder why ? -- Renxiang Yan From bugzilla-daemon at portal.open-bio.org Mon Jan 12 03:31:50 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sun, 11 Jan 2009 22:31:50 -0500 Subject: [Biojava-dev] [Bug 2536] GenBankFormat Doesn't Support Bond Features In-Reply-To: Message-ID: <200901120331.n0C3Voq9022652@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2536 ------- Comment #7 from james at carmanconsulting.com 2009-01-11 22:31 EST ------- Should this be included in the latest 1.6 release? I seem to be having the issue with the 1.6.1 version that I've downloaded. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From ola.spjuth at farmbio.uu.se Tue Jan 13 07:38:34 2009 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Tue, 13 Jan 2009 08:38:34 +0100 Subject: [Biojava-dev] XML Schema Message-ID: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> Hi, Does it exist an XML Schema (or compatible) for Biojava, or even better a common schema for the Bio* projects? If not, is this in the pipe for Biojava3? /Ola From markjschreiber at gmail.com Tue Jan 13 10:24:54 2009 From: markjschreiber at gmail.com (Mark Schreiber) Date: Tue, 13 Jan 2009 18:24:54 +0800 Subject: [Biojava-dev] XML Schema In-Reply-To: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> References: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> Message-ID: <93b45ca50901130224x3eb19fdm1dcbe3487c2aba21@mail.gmail.com> The plan for biojava3 is that most or all of it will be POJO enough to support JAXB binding. The JPA implementation of BioSQL objects in BJ3 is already XML compatible as the objects are entity beans and can be transported via JAX-RPC. - Mark On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth wrote: > > Hi, > > Does it exist an XML Schema (or compatible) for Biojava, or even better a common schema for the Bio* projects? If not, is this in the pipe for Biojava3? > > /Ola > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev From ola.spjuth at farmbio.uu.se Tue Jan 13 11:46:50 2009 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Tue, 13 Jan 2009 12:46:50 +0100 Subject: [Biojava-dev] XML Schema In-Reply-To: <93b45ca50901130224x3eb19fdm1dcbe3487c2aba21@mail.gmail.com> References: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> <93b45ca50901130224x3eb19fdm1dcbe3487c2aba21@mail.gmail.com> Message-ID: <38E3B89D-0672-49BC-85F2-C8D579CEA260@farmbio.uu.se> Hi Mark, Thanks for the quick answer. Never used JAXB myself; does this procedure support generation of an XML schema from code? I assume you will annotate the POJO's with JAXB metadata? I usually work the other way around and generate my model code from a model (usually based on an XML Schema), I guess in the end it boils down to the same result? Anyway, what is the preferred way of serializing current Biojava(X) objects to XML? Via BioSQL in some way? Cheers, /Ola On 13 jan 2009, at 11.24, Mark Schreiber wrote: > The plan for biojava3 is that most or all of it will be POJO enough to > support JAXB binding. The JPA implementation of BioSQL objects in BJ3 > is already XML compatible as the objects are entity beans and can be > transported via JAX-RPC. > > - Mark > > On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth > wrote: >> >> Hi, >> >> Does it exist an XML Schema (or compatible) for Biojava, or even >> better a common schema for the Bio* projects? If not, is this in >> the pipe for Biojava3? >> >> /Ola >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev From markjschreiber at gmail.com Tue Jan 13 12:52:38 2009 From: markjschreiber at gmail.com (Mark Schreiber) Date: Tue, 13 Jan 2009 20:52:38 +0800 Subject: [Biojava-dev] XML Schema In-Reply-To: <38E3B89D-0672-49BC-85F2-C8D579CEA260@farmbio.uu.se> References: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> <93b45ca50901130224x3eb19fdm1dcbe3487c2aba21@mail.gmail.com> <38E3B89D-0672-49BC-85F2-C8D579CEA260@farmbio.uu.se> Message-ID: <93b45ca50901130452w202b7828t87b6b03a5b2b59ad@mail.gmail.com> Hi - With JAXB you can annotate the POJOs with JAXB instructions although I believe if you have a beany object and no annotation you get default behavior if you don't annotate it. I think you can get a schema from an object or auto generate objects from a schema (unless it is a bit complex in which case you might need to put JAXB tags in the schema). There is no clearcut way to get from biojavax to XML. This is because of the heavy use of singletons and non-bean like objects in biojavax (something that BJ3 will hopefully get away from). If you want to make a custom XML serializer/ deserializer my recommendation would be to put in a middle (transport) layer of beans that operate like the DTO's of older EJB designs. They would basically be data holders that you can generate from biojavax objects and then send to XML. Going the other way you would generate these beans from XML and then use the beans to generate biojavax objects (with singletons etc). - Mark On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth wrote: > Hi Mark, > > Thanks for the quick answer. Never used JAXB myself; does this procedure > support generation of an XML schema from code? I assume you will annotate > the POJO's with JAXB metadata? I usually work the other way around and > generate my model code from a model (usually based on an XML Schema), I > guess in the end it boils down to the same result? > > Anyway, what is the preferred way of serializing current Biojava(X) objects > to XML? Via BioSQL in some way? > > Cheers, > > /Ola > > On 13 jan 2009, at 11.24, Mark Schreiber wrote: > >> The plan for biojava3 is that most or all of it will be POJO enough to >> support JAXB binding. The JPA implementation of BioSQL objects in BJ3 >> is already XML compatible as the objects are entity beans and can be >> transported via JAX-RPC. >> >> - Mark >> >> On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth >> wrote: >>> >>> Hi, >>> >>> Does it exist an XML Schema (or compatible) for Biojava, or even better a >>> common schema for the Bio* projects? If not, is this in the pipe for >>> Biojava3? >>> >>> /Ola >>> >>> _______________________________________________ >>> biojava-dev mailing list >>> biojava-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev > > From markjschreiber at gmail.com Tue Jan 13 12:54:10 2009 From: markjschreiber at gmail.com (Mark Schreiber) Date: Tue, 13 Jan 2009 20:54:10 +0800 Subject: [Biojava-dev] XML Schema In-Reply-To: <93b45ca50901130452w202b7828t87b6b03a5b2b59ad@mail.gmail.com> References: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> <93b45ca50901130224x3eb19fdm1dcbe3487c2aba21@mail.gmail.com> <38E3B89D-0672-49BC-85F2-C8D579CEA260@farmbio.uu.se> <93b45ca50901130452w202b7828t87b6b03a5b2b59ad@mail.gmail.com> Message-ID: <93b45ca50901130454r1d9aa223j5646897950389108@mail.gmail.com> Note that you could easily use the BJ3 BioSQL entity beans as the DTO layer for biojavax if you wanted to write methods to convert biojavax to the entity beans (shouldn't be hard as there is a very close relationship). - Mark On Tue, Jan 13, 2009 at 8:52 PM, Mark Schreiber wrote: > Hi - > > With JAXB you can annotate the POJOs with JAXB instructions although I > believe if you have a beany object and no annotation you get default > behavior if you don't annotate it. I think you can get a schema from > an object or auto generate objects from a schema (unless it is a bit > complex in which case you might need to put JAXB tags in the schema). > > There is no clearcut way to get from biojavax to XML. This is because > of the heavy use of singletons and non-bean like objects in biojavax > (something that BJ3 will hopefully get away from). If you want to make > a custom XML serializer/ deserializer my recommendation would be to > put in a middle (transport) layer of beans that operate like the DTO's > of older EJB designs. They would basically be data holders that you > can generate from biojavax objects and then send to XML. Going the > other way you would generate these beans from XML and then use the > beans to generate biojavax objects (with singletons etc). > > - Mark > > On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth wrote: >> Hi Mark, >> >> Thanks for the quick answer. Never used JAXB myself; does this procedure >> support generation of an XML schema from code? I assume you will annotate >> the POJO's with JAXB metadata? I usually work the other way around and >> generate my model code from a model (usually based on an XML Schema), I >> guess in the end it boils down to the same result? >> >> Anyway, what is the preferred way of serializing current Biojava(X) objects >> to XML? Via BioSQL in some way? >> >> Cheers, >> >> /Ola >> >> On 13 jan 2009, at 11.24, Mark Schreiber wrote: >> >>> The plan for biojava3 is that most or all of it will be POJO enough to >>> support JAXB binding. The JPA implementation of BioSQL objects in BJ3 >>> is already XML compatible as the objects are entity beans and can be >>> transported via JAX-RPC. >>> >>> - Mark >>> >>> On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth >>> wrote: >>>> >>>> Hi, >>>> >>>> Does it exist an XML Schema (or compatible) for Biojava, or even better a >>>> common schema for the Bio* projects? If not, is this in the pipe for >>>> Biojava3? >>>> >>>> /Ola >>>> >>>> _______________________________________________ >>>> biojava-dev mailing list >>>> biojava-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> >> > From ola.spjuth at farmbio.uu.se Tue Jan 13 13:47:53 2009 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Tue, 13 Jan 2009 14:47:53 +0100 Subject: [Biojava-dev] XML Schema In-Reply-To: <93b45ca50901130452w202b7828t87b6b03a5b2b59ad@mail.gmail.com> References: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> <93b45ca50901130224x3eb19fdm1dcbe3487c2aba21@mail.gmail.com> <38E3B89D-0672-49BC-85F2-C8D579CEA260@farmbio.uu.se> <93b45ca50901130452w202b7828t87b6b03a5b2b59ad@mail.gmail.com> Message-ID: Hi, Seems a bit too time-consuming for me for the moment, I'll have to wait for BJ3. Is there a roadmap/timeframe for this? I just want to suggest (for BJ3 development) to have/generate an XML Schema. At least I would benefit from this since I generate service bindings on the fly and also want to validate data in remote services. Cheers, /Ola On 13 jan 2009, at 13.52, Mark Schreiber wrote: > Hi - > > With JAXB you can annotate the POJOs with JAXB instructions although I > believe if you have a beany object and no annotation you get default > behavior if you don't annotate it. I think you can get a schema from > an object or auto generate objects from a schema (unless it is a bit > complex in which case you might need to put JAXB tags in the schema). > > There is no clearcut way to get from biojavax to XML. This is because > of the heavy use of singletons and non-bean like objects in biojavax > (something that BJ3 will hopefully get away from). If you want to make > a custom XML serializer/ deserializer my recommendation would be to > put in a middle (transport) layer of beans that operate like the DTO's > of older EJB designs. They would basically be data holders that you > can generate from biojavax objects and then send to XML. Going the > other way you would generate these beans from XML and then use the > beans to generate biojavax objects (with singletons etc). > > - Mark > > On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth > wrote: >> Hi Mark, >> >> Thanks for the quick answer. Never used JAXB myself; does this >> procedure >> support generation of an XML schema from code? I assume you will >> annotate >> the POJO's with JAXB metadata? I usually work the other way around >> and >> generate my model code from a model (usually based on an XML >> Schema), I >> guess in the end it boils down to the same result? >> >> Anyway, what is the preferred way of serializing current Biojava(X) >> objects >> to XML? Via BioSQL in some way? >> >> Cheers, >> >> /Ola >> >> On 13 jan 2009, at 11.24, Mark Schreiber wrote: >> >>> The plan for biojava3 is that most or all of it will be POJO >>> enough to >>> support JAXB binding. The JPA implementation of BioSQL objects in >>> BJ3 >>> is already XML compatible as the objects are entity beans and can be >>> transported via JAX-RPC. >>> >>> - Mark >>> >>> On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth >> > >>> wrote: >>>> >>>> Hi, >>>> >>>> Does it exist an XML Schema (or compatible) for Biojava, or even >>>> better a >>>> common schema for the Bio* projects? If not, is this in the pipe >>>> for >>>> Biojava3? >>>> >>>> /Ola >>>> >>>> _______________________________________________ >>>> biojava-dev mailing list >>>> biojava-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> >> From holland at eaglegenomics.com Tue Jan 13 13:47:42 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Tue, 13 Jan 2009 13:47:42 +0000 Subject: [Biojava-dev] XML Schema In-Reply-To: References: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> <93b45ca50901130224x3eb19fdm1dcbe3487c2aba21@mail.gmail.com> <38E3B89D-0672-49BC-85F2-C8D579CEA260@farmbio.uu.se> <93b45ca50901130452w202b7828t87b6b03a5b2b59ad@mail.gmail.com> Message-ID: <496C9B7E.2030600@eaglegenomics.com> Sorry about that last one. I understand what you're getting at now. There is no current roadmap/timeline for BJ3 as there is nobody developing it except me and I've got lots of other things to do at the moment, which involve getting paid and so sadly have to take priority. Maybe there is someone out there who is willing to take responsibility for it and project manage the BJ3 development? cheers, Richard Ola Spjuth wrote: > Hi, > > Seems a bit too time-consuming for me for the moment, I'll have to wait > for BJ3. Is there a roadmap/timeframe for this? > > I just want to suggest (for BJ3 development) to have/generate an XML > Schema. At least I would benefit from this since I generate service > bindings on the fly and also want to validate data in remote services. > > Cheers, > > /Ola > > On 13 jan 2009, at 13.52, Mark Schreiber wrote: > >> Hi - >> >> With JAXB you can annotate the POJOs with JAXB instructions although I >> believe if you have a beany object and no annotation you get default >> behavior if you don't annotate it. I think you can get a schema from >> an object or auto generate objects from a schema (unless it is a bit >> complex in which case you might need to put JAXB tags in the schema). >> >> There is no clearcut way to get from biojavax to XML. This is because >> of the heavy use of singletons and non-bean like objects in biojavax >> (something that BJ3 will hopefully get away from). If you want to make >> a custom XML serializer/ deserializer my recommendation would be to >> put in a middle (transport) layer of beans that operate like the DTO's >> of older EJB designs. They would basically be data holders that you >> can generate from biojavax objects and then send to XML. Going the >> other way you would generate these beans from XML and then use the >> beans to generate biojavax objects (with singletons etc). >> >> - Mark >> >> On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth >> wrote: >>> Hi Mark, >>> >>> Thanks for the quick answer. Never used JAXB myself; does this procedure >>> support generation of an XML schema from code? I assume you will >>> annotate >>> the POJO's with JAXB metadata? I usually work the other way around and >>> generate my model code from a model (usually based on an XML Schema), I >>> guess in the end it boils down to the same result? >>> >>> Anyway, what is the preferred way of serializing current Biojava(X) >>> objects >>> to XML? Via BioSQL in some way? >>> >>> Cheers, >>> >>> /Ola >>> >>> On 13 jan 2009, at 11.24, Mark Schreiber wrote: >>> >>>> The plan for biojava3 is that most or all of it will be POJO enough to >>>> support JAXB binding. The JPA implementation of BioSQL objects in BJ3 >>>> is already XML compatible as the objects are entity beans and can be >>>> transported via JAX-RPC. >>>> >>>> - Mark >>>> >>>> On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth >>>> wrote: >>>>> >>>>> Hi, >>>>> >>>>> Does it exist an XML Schema (or compatible) for Biojava, or even >>>>> better a >>>>> common schema for the Bio* projects? If not, is this in the pipe for >>>>> Biojava3? >>>>> >>>>> /Ola >>>>> >>>>> _______________________________________________ >>>>> biojava-dev mailing list >>>>> biojava-dev at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>> >>> > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From markjschreiber at gmail.com Tue Jan 13 14:03:26 2009 From: markjschreiber at gmail.com (markjschreiber at gmail.com) Date: Tue, 13 Jan 2009 14:03:26 +0000 Subject: [Biojava-dev] XML Schema Message-ID: <00163646ccdeea728e04605dafcc@google.com> It would probably be less time consuming to write the bridge than wait for BJ3 which has no time frame as yet. I also don't think there will be (or should be) a unified XML schema for BJ3 as it will be much more modular (by design). Possibly each module could have a schema if relevant. Generally it is hoped that each module will be compatible with bean like design (unless there is a good reason not to) so this would implicitly mean there will be simple XML schema generation. - Mark On Jan 13, 2009 9:47pm, Ola Spjuth wrote: > Hi, > > > > Seems a bit too time-consuming for me for the moment, I'll have to wait for BJ3. Is there a roadmap/timeframe for this? > > > > I just want to suggest (for BJ3 development) to have/generate an XML Schema. At least I would benefit from this since I generate service bindings on the fly and also want to validate data in remote services. > > > > Cheers, > > > > /Ola > > > > On 13 jan 2009, at 13.52, Mark Schreiber wrote: > > > > > Hi - > > > > With JAXB you can annotate the POJOs with JAXB instructions although I > > believe if you have a beany object and no annotation you get default > > behavior if you don't annotate it. I think you can get a schema from > > an object or auto generate objects from a schema (unless it is a bit > > complex in which case you might need to put JAXB tags in the schema). > > > > There is no clearcut way to get from biojavax to XML. This is because > > of the heavy use of singletons and non-bean like objects in biojavax > > (something that BJ3 will hopefully get away from). If you want to make > > a custom XML serializer/ deserializer my recommendation would be to > > put in a middle (transport) layer of beans that operate like the DTO's > > of older EJB designs. They would basically be data holders that you > > can generate from biojavax objects and then send to XML. Going the > > other way you would generate these beans from XML and then use the > > beans to generate biojavax objects (with singletons etc). > > > > - Mark > > > > On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth ola.spjuth at farmbio.uu.se> wrote: > > > Hi Mark, > > > > Thanks for the quick answer. Never used JAXB myself; does this procedure > > support generation of an XML schema from code? I assume you will annotate > > the POJO's with JAXB metadata? I usually work the other way around and > > generate my model code from a model (usually based on an XML Schema), I > > guess in the end it boils down to the same result? > > > > Anyway, what is the preferred way of serializing current Biojava(X) objects > > to XML? Via BioSQL in some way? > > > > Cheers, > > > > /Ola > > > > On 13 jan 2009, at 11.24, Mark Schreiber wrote: > > > > > The plan for biojava3 is that most or all of it will be POJO enough to > > support JAXB binding. The JPA implementation of BioSQL objects in BJ3 > > is already XML compatible as the objects are entity beans and can be > > transported via JAX-RPC. > > > > - Mark > > > > On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth ola.spjuth at farmbio.uu.se> > > wrote: > > > > > Hi, > > > > Does it exist an XML Schema (or compatible) for Biojava, or even better a > > common schema for the Bio* projects? If not, is this in the pipe for > > Biojava3? > > > > /Ola > > > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > > > > > > > > From holland at eaglegenomics.com Tue Jan 13 13:15:51 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Tue, 13 Jan 2009 13:15:51 +0000 Subject: [Biojava-dev] XML Schema In-Reply-To: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> References: <8142E3D9-515D-4634-A9A8-DA671C45939F@farmbio.uu.se> Message-ID: <496C9407.4090401@eaglegenomics.com> I don't understand your request. XML Schemas are for describing XML documents. BioJava is not an XML document, it is a piece of Java software! cheers, Richard Ola Spjuth wrote: > Hi, > > Does it exist an XML Schema (or compatible) for Biojava, or even better > a common schema for the Bio* projects? If not, is this in the pipe for > Biojava3? > > /Ola > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From TSN at atp.dk Tue Jan 13 14:24:31 2009 From: TSN at atp.dk (TSN at atp.dk) Date: Tue, 13 Jan 2009 15:24:31 +0100 Subject: [Biojava-dev] Vedr.: biojava-dev Digest, Vol 70, Issue 2 In-Reply-To: Message-ID: Hello ! Regarding XML-Schemas - Have You ever tried to use XML-beans. As a proffesional JAVA developer I have had some very good experiences in converting between JAVA objects and complex XML structures with XML-beans. You have to setup a system for generating the beans, but afterwards the benefir is worth it /Tom Stevns - DK biojava-dev-request at lists.open-bio.org Sendt af: biojava-dev-bounces at lists.open-bio.org 13-01-2009 15:03 Besvar venligst til biojava-dev at lists.open-bio.org Til biojava-dev at lists.open-bio.org cc Emne biojava-dev Digest, Vol 70, Issue 2 Send biojava-dev mailing list submissions to biojava-dev at lists.open-bio.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.open-bio.org/mailman/listinfo/biojava-dev or, via email, send a message with subject or body 'help' to biojava-dev-request at lists.open-bio.org You can reach the person managing the list at biojava-dev-owner at lists.open-bio.org When replying, please edit your Subject line so it is more specific than "Re: Contents of biojava-dev digest..." Today's Topics: 1. Re: XML Schema (Mark Schreiber) 2. Re: XML Schema (Ola Spjuth) 3. Re: XML Schema (Mark Schreiber) 4. Re: XML Schema (Mark Schreiber) 5. Re: XML Schema (Ola Spjuth) 6. Re: XML Schema (Richard Holland) 7. Re: XML Schema (markjschreiber at gmail.com) ---------------------------------------------------------------------- Message: 1 Date: Tue, 13 Jan 2009 18:24:54 +0800 From: "Mark Schreiber" Subject: Re: [Biojava-dev] XML Schema To: "Ola Spjuth" Cc: biojava-dev at biojava.org Message-ID: <93b45ca50901130224x3eb19fdm1dcbe3487c2aba21 at mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 The plan for biojava3 is that most or all of it will be POJO enough to support JAXB binding. The JPA implementation of BioSQL objects in BJ3 is already XML compatible as the objects are entity beans and can be transported via JAX-RPC. - Mark On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth wrote: > > Hi, > > Does it exist an XML Schema (or compatible) for Biojava, or even better a common schema for the Bio* projects? If not, is this in the pipe for Biojava3? > > /Ola > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev ------------------------------ Message: 2 Date: Tue, 13 Jan 2009 12:46:50 +0100 From: Ola Spjuth Subject: Re: [Biojava-dev] XML Schema To: Mark Schreiber Cc: biojava-dev at biojava.org Message-ID: <38E3B89D-0672-49BC-85F2-C8D579CEA260 at farmbio.uu.se> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Hi Mark, Thanks for the quick answer. Never used JAXB myself; does this procedure support generation of an XML schema from code? I assume you will annotate the POJO's with JAXB metadata? I usually work the other way around and generate my model code from a model (usually based on an XML Schema), I guess in the end it boils down to the same result? Anyway, what is the preferred way of serializing current Biojava(X) objects to XML? Via BioSQL in some way? Cheers, /Ola On 13 jan 2009, at 11.24, Mark Schreiber wrote: > The plan for biojava3 is that most or all of it will be POJO enough to > support JAXB binding. The JPA implementation of BioSQL objects in BJ3 > is already XML compatible as the objects are entity beans and can be > transported via JAX-RPC. > > - Mark > > On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth > wrote: >> >> Hi, >> >> Does it exist an XML Schema (or compatible) for Biojava, or even >> better a common schema for the Bio* projects? If not, is this in >> the pipe for Biojava3? >> >> /Ola >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev ------------------------------ Message: 3 Date: Tue, 13 Jan 2009 20:52:38 +0800 From: "Mark Schreiber" Subject: Re: [Biojava-dev] XML Schema To: "Ola Spjuth" Cc: biojava-dev at biojava.org Message-ID: <93b45ca50901130452w202b7828t87b6b03a5b2b59ad at mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi - With JAXB you can annotate the POJOs with JAXB instructions although I believe if you have a beany object and no annotation you get default behavior if you don't annotate it. I think you can get a schema from an object or auto generate objects from a schema (unless it is a bit complex in which case you might need to put JAXB tags in the schema). There is no clearcut way to get from biojavax to XML. This is because of the heavy use of singletons and non-bean like objects in biojavax (something that BJ3 will hopefully get away from). If you want to make a custom XML serializer/ deserializer my recommendation would be to put in a middle (transport) layer of beans that operate like the DTO's of older EJB designs. They would basically be data holders that you can generate from biojavax objects and then send to XML. Going the other way you would generate these beans from XML and then use the beans to generate biojavax objects (with singletons etc). - Mark On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth wrote: > Hi Mark, > > Thanks for the quick answer. Never used JAXB myself; does this procedure > support generation of an XML schema from code? I assume you will annotate > the POJO's with JAXB metadata? I usually work the other way around and > generate my model code from a model (usually based on an XML Schema), I > guess in the end it boils down to the same result? > > Anyway, what is the preferred way of serializing current Biojava(X) objects > to XML? Via BioSQL in some way? > > Cheers, > > /Ola > > On 13 jan 2009, at 11.24, Mark Schreiber wrote: > >> The plan for biojava3 is that most or all of it will be POJO enough to >> support JAXB binding. The JPA implementation of BioSQL objects in BJ3 >> is already XML compatible as the objects are entity beans and can be >> transported via JAX-RPC. >> >> - Mark >> >> On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth >> wrote: >>> >>> Hi, >>> >>> Does it exist an XML Schema (or compatible) for Biojava, or even better a >>> common schema for the Bio* projects? If not, is this in the pipe for >>> Biojava3? >>> >>> /Ola >>> >>> _______________________________________________ >>> biojava-dev mailing list >>> biojava-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev > > ------------------------------ Message: 4 Date: Tue, 13 Jan 2009 20:54:10 +0800 From: "Mark Schreiber" Subject: Re: [Biojava-dev] XML Schema To: "Ola Spjuth" Cc: biojava-dev at biojava.org Message-ID: <93b45ca50901130454r1d9aa223j5646897950389108 at mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Note that you could easily use the BJ3 BioSQL entity beans as the DTO layer for biojavax if you wanted to write methods to convert biojavax to the entity beans (shouldn't be hard as there is a very close relationship). - Mark On Tue, Jan 13, 2009 at 8:52 PM, Mark Schreiber wrote: > Hi - > > With JAXB you can annotate the POJOs with JAXB instructions although I > believe if you have a beany object and no annotation you get default > behavior if you don't annotate it. I think you can get a schema from > an object or auto generate objects from a schema (unless it is a bit > complex in which case you might need to put JAXB tags in the schema). > > There is no clearcut way to get from biojavax to XML. This is because > of the heavy use of singletons and non-bean like objects in biojavax > (something that BJ3 will hopefully get away from). If you want to make > a custom XML serializer/ deserializer my recommendation would be to > put in a middle (transport) layer of beans that operate like the DTO's > of older EJB designs. They would basically be data holders that you > can generate from biojavax objects and then send to XML. Going the > other way you would generate these beans from XML and then use the > beans to generate biojavax objects (with singletons etc). > > - Mark > > On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth wrote: >> Hi Mark, >> >> Thanks for the quick answer. Never used JAXB myself; does this procedure >> support generation of an XML schema from code? I assume you will annotate >> the POJO's with JAXB metadata? I usually work the other way around and >> generate my model code from a model (usually based on an XML Schema), I >> guess in the end it boils down to the same result? >> >> Anyway, what is the preferred way of serializing current Biojava(X) objects >> to XML? Via BioSQL in some way? >> >> Cheers, >> >> /Ola >> >> On 13 jan 2009, at 11.24, Mark Schreiber wrote: >> >>> The plan for biojava3 is that most or all of it will be POJO enough to >>> support JAXB binding. The JPA implementation of BioSQL objects in BJ3 >>> is already XML compatible as the objects are entity beans and can be >>> transported via JAX-RPC. >>> >>> - Mark >>> >>> On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth >>> wrote: >>>> >>>> Hi, >>>> >>>> Does it exist an XML Schema (or compatible) for Biojava, or even better a >>>> common schema for the Bio* projects? If not, is this in the pipe for >>>> Biojava3? >>>> >>>> /Ola >>>> >>>> _______________________________________________ >>>> biojava-dev mailing list >>>> biojava-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> >> > ------------------------------ Message: 5 Date: Tue, 13 Jan 2009 14:47:53 +0100 From: Ola Spjuth Subject: Re: [Biojava-dev] XML Schema To: Mark Schreiber Cc: biojava-dev at biojava.org Message-ID: Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Hi, Seems a bit too time-consuming for me for the moment, I'll have to wait for BJ3. Is there a roadmap/timeframe for this? I just want to suggest (for BJ3 development) to have/generate an XML Schema. At least I would benefit from this since I generate service bindings on the fly and also want to validate data in remote services. Cheers, /Ola On 13 jan 2009, at 13.52, Mark Schreiber wrote: > Hi - > > With JAXB you can annotate the POJOs with JAXB instructions although I > believe if you have a beany object and no annotation you get default > behavior if you don't annotate it. I think you can get a schema from > an object or auto generate objects from a schema (unless it is a bit > complex in which case you might need to put JAXB tags in the schema). > > There is no clearcut way to get from biojavax to XML. This is because > of the heavy use of singletons and non-bean like objects in biojavax > (something that BJ3 will hopefully get away from). If you want to make > a custom XML serializer/ deserializer my recommendation would be to > put in a middle (transport) layer of beans that operate like the DTO's > of older EJB designs. They would basically be data holders that you > can generate from biojavax objects and then send to XML. Going the > other way you would generate these beans from XML and then use the > beans to generate biojavax objects (with singletons etc). > > - Mark > > On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth > wrote: >> Hi Mark, >> >> Thanks for the quick answer. Never used JAXB myself; does this >> procedure >> support generation of an XML schema from code? I assume you will >> annotate >> the POJO's with JAXB metadata? I usually work the other way around >> and >> generate my model code from a model (usually based on an XML >> Schema), I >> guess in the end it boils down to the same result? >> >> Anyway, what is the preferred way of serializing current Biojava(X) >> objects >> to XML? Via BioSQL in some way? >> >> Cheers, >> >> /Ola >> >> On 13 jan 2009, at 11.24, Mark Schreiber wrote: >> >>> The plan for biojava3 is that most or all of it will be POJO >>> enough to >>> support JAXB binding. The JPA implementation of BioSQL objects in >>> BJ3 >>> is already XML compatible as the objects are entity beans and can be >>> transported via JAX-RPC. >>> >>> - Mark >>> >>> On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth >> > >>> wrote: >>>> >>>> Hi, >>>> >>>> Does it exist an XML Schema (or compatible) for Biojava, or even >>>> better a >>>> common schema for the Bio* projects? If not, is this in the pipe >>>> for >>>> Biojava3? >>>> >>>> /Ola >>>> >>>> _______________________________________________ >>>> biojava-dev mailing list >>>> biojava-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> >> ------------------------------ Message: 6 Date: Tue, 13 Jan 2009 13:47:42 +0000 From: Richard Holland Subject: Re: [Biojava-dev] XML Schema To: Ola Spjuth Cc: biojava-dev at biojava.org Message-ID: <496C9B7E.2030600 at eaglegenomics.com> Content-Type: text/plain; charset=ISO-8859-1 Sorry about that last one. I understand what you're getting at now. There is no current roadmap/timeline for BJ3 as there is nobody developing it except me and I've got lots of other things to do at the moment, which involve getting paid and so sadly have to take priority. Maybe there is someone out there who is willing to take responsibility for it and project manage the BJ3 development? cheers, Richard Ola Spjuth wrote: > Hi, > > Seems a bit too time-consuming for me for the moment, I'll have to wait > for BJ3. Is there a roadmap/timeframe for this? > > I just want to suggest (for BJ3 development) to have/generate an XML > Schema. At least I would benefit from this since I generate service > bindings on the fly and also want to validate data in remote services. > > Cheers, > > /Ola > > On 13 jan 2009, at 13.52, Mark Schreiber wrote: > >> Hi - >> >> With JAXB you can annotate the POJOs with JAXB instructions although I >> believe if you have a beany object and no annotation you get default >> behavior if you don't annotate it. I think you can get a schema from >> an object or auto generate objects from a schema (unless it is a bit >> complex in which case you might need to put JAXB tags in the schema). >> >> There is no clearcut way to get from biojavax to XML. This is because >> of the heavy use of singletons and non-bean like objects in biojavax >> (something that BJ3 will hopefully get away from). If you want to make >> a custom XML serializer/ deserializer my recommendation would be to >> put in a middle (transport) layer of beans that operate like the DTO's >> of older EJB designs. They would basically be data holders that you >> can generate from biojavax objects and then send to XML. Going the >> other way you would generate these beans from XML and then use the >> beans to generate biojavax objects (with singletons etc). >> >> - Mark >> >> On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth >> wrote: >>> Hi Mark, >>> >>> Thanks for the quick answer. Never used JAXB myself; does this procedure >>> support generation of an XML schema from code? I assume you will >>> annotate >>> the POJO's with JAXB metadata? I usually work the other way around and >>> generate my model code from a model (usually based on an XML Schema), I >>> guess in the end it boils down to the same result? >>> >>> Anyway, what is the preferred way of serializing current Biojava(X) >>> objects >>> to XML? Via BioSQL in some way? >>> >>> Cheers, >>> >>> /Ola >>> >>> On 13 jan 2009, at 11.24, Mark Schreiber wrote: >>> >>>> The plan for biojava3 is that most or all of it will be POJO enough to >>>> support JAXB binding. The JPA implementation of BioSQL objects in BJ3 >>>> is already XML compatible as the objects are entity beans and can be >>>> transported via JAX-RPC. >>>> >>>> - Mark >>>> >>>> On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth >>>> wrote: >>>>> >>>>> Hi, >>>>> >>>>> Does it exist an XML Schema (or compatible) for Biojava, or even >>>>> better a >>>>> common schema for the Bio* projects? If not, is this in the pipe for >>>>> Biojava3? >>>>> >>>>> /Ola >>>>> >>>>> _______________________________________________ >>>>> biojava-dev mailing list >>>>> biojava-dev at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>> >>> > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ ------------------------------ Message: 7 Date: Tue, 13 Jan 2009 14:03:26 +0000 From: markjschreiber at gmail.com Subject: Re: [Biojava-dev] XML Schema To: Ola Spjuth , Mark Schreiber , biojava-dev at biojava.org Message-ID: <00163646ccdeea728e04605dafcc at google.com> Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes It would probably be less time consuming to write the bridge than wait for BJ3 which has no time frame as yet. I also don't think there will be (or should be) a unified XML schema for BJ3 as it will be much more modular (by design). Possibly each module could have a schema if relevant. Generally it is hoped that each module will be compatible with bean like design (unless there is a good reason not to) so this would implicitly mean there will be simple XML schema generation. - Mark On Jan 13, 2009 9:47pm, Ola Spjuth wrote: > Hi, > > > > Seems a bit too time-consuming for me for the moment, I'll have to wait for BJ3. Is there a roadmap/timeframe for this? > > > > I just want to suggest (for BJ3 development) to have/generate an XML Schema. At least I would benefit from this since I generate service bindings on the fly and also want to validate data in remote services. > > > > Cheers, > > > > /Ola > > > > On 13 jan 2009, at 13.52, Mark Schreiber wrote: > > > > > Hi - > > > > With JAXB you can annotate the POJOs with JAXB instructions although I > > believe if you have a beany object and no annotation you get default > > behavior if you don't annotate it. I think you can get a schema from > > an object or auto generate objects from a schema (unless it is a bit > > complex in which case you might need to put JAXB tags in the schema). > > > > There is no clearcut way to get from biojavax to XML. This is because > > of the heavy use of singletons and non-bean like objects in biojavax > > (something that BJ3 will hopefully get away from). If you want to make > > a custom XML serializer/ deserializer my recommendation would be to > > put in a middle (transport) layer of beans that operate like the DTO's > > of older EJB designs. They would basically be data holders that you > > can generate from biojavax objects and then send to XML. Going the > > other way you would generate these beans from XML and then use the > > beans to generate biojavax objects (with singletons etc). > > > > - Mark > > > > On Tue, Jan 13, 2009 at 7:46 PM, Ola Spjuth ola.spjuth at farmbio.uu.se> wrote: > > > Hi Mark, > > > > Thanks for the quick answer. Never used JAXB myself; does this procedure > > support generation of an XML schema from code? I assume you will annotate > > the POJO's with JAXB metadata? I usually work the other way around and > > generate my model code from a model (usually based on an XML Schema), I > > guess in the end it boils down to the same result? > > > > Anyway, what is the preferred way of serializing current Biojava(X) objects > > to XML? Via BioSQL in some way? > > > > Cheers, > > > > /Ola > > > > On 13 jan 2009, at 11.24, Mark Schreiber wrote: > > > > > The plan for biojava3 is that most or all of it will be POJO enough to > > support JAXB binding. The JPA implementation of BioSQL objects in BJ3 > > is already XML compatible as the objects are entity beans and can be > > transported via JAX-RPC. > > > > - Mark > > > > On Tue, Jan 13, 2009 at 3:38 PM, Ola Spjuth ola.spjuth at farmbio.uu.se> > > wrote: > > > > > Hi, > > > > Does it exist an XML Schema (or compatible) for Biojava, or even better a > > common schema for the Bio* projects? If not, is this in the pipe for > > Biojava3? > > > > /Ola > > > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > > > > > > > > ------------------------------ _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev End of biojava-dev Digest, Vol 70, Issue 2 ****************************************** From james at carmanconsulting.com Thu Jan 15 12:06:33 2009 From: james at carmanconsulting.com (James Carman) Date: Thu, 15 Jan 2009 07:06:33 -0500 Subject: [Biojava-dev] Bug 2536... Message-ID: The patch I supplied was supposed to be applied for bug: http://bugzilla.open-bio.org/show_bug.cgi?id=2536 However, I have downloaded the latest 1.6.1 release and it looks like I'm still having the same issues. Was the patch not applied to that branch or something? James From andreas at sdsc.edu Thu Jan 15 13:50:36 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 15 Jan 2009 14:50:36 +0100 Subject: [Biojava-dev] Bug 2536... In-Reply-To: References: Message-ID: <59a41c430901150550m75a772c3ueb51934cbaccb092@mail.gmail.com> Hi James, I applied your patch on July 4th 2008 (revision 4825). The 1.6 release was branched before that date. As such your patch is available via a recent SVN checkout and will become part of the next biojava 1.7. We don't have a release plan for that yet, but traditionally we do a release at some point before ISMB in late spring/early summer. Andreas On Thu, Jan 15, 2009 at 1:06 PM, James Carman wrote: > The patch I supplied was supposed to be applied for bug: > > http://bugzilla.open-bio.org/show_bug.cgi?id=2536 > > However, I have downloaded the latest 1.6.1 release and it looks like > I'm still having the same issues. Was the patch not applied to that > branch or something? > > James > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From james at carmanconsulting.com Thu Jan 15 14:30:22 2009 From: james at carmanconsulting.com (James Carman) Date: Thu, 15 Jan 2009 09:30:22 -0500 Subject: [Biojava-dev] Bug 2536... In-Reply-To: <59a41c430901150546v516208b5k203ba3cab2169eb1@mail.gmail.com> References: <59a41c430901150546v516208b5k203ba3cab2169eb1@mail.gmail.com> Message-ID: Ok, great. I guess we'll just do an internal 1.7 release, then. Thanks for the info! On Thu, Jan 15, 2009 at 8:46 AM, Andreas Prlic wrote: > Hi James, > > I applied your patch on July 4th 2008 (revision 4825). The 1.6 release > was branched before that date. As such your patch is available via a > recent SVN checkout and will become part of the next biojava 1.7. We > don't have a release plan for that yet, but traditionally we do a > release at some point before ISMB in late spring/early summer. > > Andreas > > On Thu, Jan 15, 2009 at 1:06 PM, James Carman > wrote: >> The patch I supplied was supposed to be applied for bug: >> >> http://bugzilla.open-bio.org/show_bug.cgi?id=2536 >> >> However, I have downloaded the latest 1.6.1 release and it looks like >> I'm still having the same issues. Was the patch not applied to that >> branch or something? >> >> James >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > From andreas at sdsc.edu Thu Jan 15 14:41:40 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 15 Jan 2009 15:41:40 +0100 Subject: [Biojava-dev] Bug 2536... In-Reply-To: References: <59a41c430901150546v516208b5k203ba3cab2169eb1@mail.gmail.com> Message-ID: <59a41c430901150641w3d7695c1kfa84e6321f924a45@mail.gmail.com> as usually you can also download a biojava.jar that is based on the latest build from http://www.spice-3d.org/cruise/ A On Thu, Jan 15, 2009 at 3:30 PM, James Carman wrote: > Ok, great. I guess we'll just do an internal 1.7 release, then. > Thanks for the info! > > On Thu, Jan 15, 2009 at 8:46 AM, Andreas Prlic wrote: >> Hi James, >> >> I applied your patch on July 4th 2008 (revision 4825). The 1.6 release >> was branched before that date. As such your patch is available via a >> recent SVN checkout and will become part of the next biojava 1.7. We >> don't have a release plan for that yet, but traditionally we do a >> release at some point before ISMB in late spring/early summer. >> >> Andreas >> >> On Thu, Jan 15, 2009 at 1:06 PM, James Carman >> wrote: >>> The patch I supplied was supposed to be applied for bug: >>> >>> http://bugzilla.open-bio.org/show_bug.cgi?id=2536 >>> >>> However, I have downloaded the latest 1.6.1 release and it looks like >>> I'm still having the same issues. Was the patch not applied to that >>> branch or something? >>> >>> James >>> _______________________________________________ >>> biojava-dev mailing list >>> biojava-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>> >> > From james at carmanconsulting.com Thu Jan 15 14:43:33 2009 From: james at carmanconsulting.com (James Carman) Date: Thu, 15 Jan 2009 09:43:33 -0500 Subject: [Biojava-dev] Bug 2536... In-Reply-To: <59a41c430901150641w3d7695c1kfa84e6321f924a45@mail.gmail.com> References: <59a41c430901150546v516208b5k203ba3cab2169eb1@mail.gmail.com> <59a41c430901150641w3d7695c1kfa84e6321f924a45@mail.gmail.com> Message-ID: Even better! Thanks, Andreas! On Thu, Jan 15, 2009 at 9:41 AM, Andreas Prlic wrote: > as usually you can also download a biojava.jar that is based on the > latest build from > http://www.spice-3d.org/cruise/ > > A > > On Thu, Jan 15, 2009 at 3:30 PM, James Carman > wrote: >> Ok, great. I guess we'll just do an internal 1.7 release, then. >> Thanks for the info! >> >> On Thu, Jan 15, 2009 at 8:46 AM, Andreas Prlic wrote: >>> Hi James, >>> >>> I applied your patch on July 4th 2008 (revision 4825). The 1.6 release >>> was branched before that date. As such your patch is available via a >>> recent SVN checkout and will become part of the next biojava 1.7. We >>> don't have a release plan for that yet, but traditionally we do a >>> release at some point before ISMB in late spring/early summer. >>> >>> Andreas >>> >>> On Thu, Jan 15, 2009 at 1:06 PM, James Carman >>> wrote: >>>> The patch I supplied was supposed to be applied for bug: >>>> >>>> http://bugzilla.open-bio.org/show_bug.cgi?id=2536 >>>> >>>> However, I have downloaded the latest 1.6.1 release and it looks like >>>> I'm still having the same issues. Was the patch not applied to that >>>> branch or something? >>>> >>>> James >>>> _______________________________________________ >>>> biojava-dev mailing list >>>> biojava-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>>> >>> >> > From bugzilla-daemon at portal.open-bio.org Fri Jan 23 13:45:19 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 23 Jan 2009 08:45:19 -0500 Subject: [Biojava-dev] [Bug 2741] New: oboFileParser - findUnescaped Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2741 Summary: oboFileParser - findUnescaped Product: BioJava Version: live (CVS source) Platform: PC OS/Version: Windows XP Status: NEW Severity: normal Priority: P2 Component: ontology AssignedTo: biojava-dev at biojava.org ReportedBy: alex.gawronski at gmail.com When the oboFileParser parser checks for quotes using findUnescaped, it never starts reading again. If there is a quote character then it ignores all the characters until it sees another quote character. The problem is that it never started reading again after it sees the second quote character. This caused the method to miss the escape character. I added "inQuotes = false;" to the findUnescaped method and it works fine. public static int findUnescaped(String str, char toChar, int startindex, int endindex, boolean honorQuotes) { boolean inQuotes = false; char quoteChar = '\0'; for (int i = startindex; i < endindex; i++) { char c = str.charAt(i); if (c == '\\') { i++; continue; } else if (inQuotes) { if (c == quoteChar) inQuotes = false; continue; } else if (c == toChar) { return i; } else if (honorQuotes && isQuote(c)) { inQuotes = true; quoteChar = c; } } return -1; } -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Jan 23 18:03:31 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 23 Jan 2009 13:03:31 -0500 Subject: [Biojava-dev] [Bug 2741] oboFileParser - findUnescaped In-Reply-To: Message-ID: <200901231803.n0NI3VRQ022333@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2741 ap3 at sanger.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #1 from ap3 at sanger.ac.uk 2009-01-23 13:03 EST ------- thanks for the patch, committed it to svn, Andreas -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From andreas at sdsc.edu Thu Jan 29 21:11:51 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 29 Jan 2009 13:11:51 -0800 Subject: [Biojava-dev] [Biojava-l] Problem with blast file parser In-Reply-To: <498217B3.4010703@Gmail.com> References: <497913F9.70009@Gmail.com> <4979ED9C.6040207@imbusch.net> <498217B3.4010703@Gmail.com> Message-ID: <59a41c430901291311w642a98am68b33cc6c78b15f1@mail.gmail.com> Hi, We had a couple of bug reports recently regarding issues that already got fixed in the latest biojava builds from SVN. I think it is time to start preparing the next biojava release ( 1.7 ) to make sure everybody gets up to the latest status... Andreas On Thu, Jan 29, 2009 at 12:55 PM, Marcel Huntemann wrote: > Hi Charles! > > I've "found" a solution now. After dealing a couple of days with the > terrible xml output of blast and BioJava's BlastXMLParser (which also > wasn't working properly), I decided to have a look at the source code and > try to figure out myself what was wrong with the BlastLikeSAXParser. So I > checked out the present status of the source code via the anonymous svn > checkout (howto here: http://biojava.org/wiki/CVS_to_SVN_Migration). After > a couple of hours and me not finding an error that could cause this > behavior, I thought I'll just give it a try and compiled the checked out > source via ant. Then used the new created biojava.jar and suddenly > everything went perfectly! > So, whatever the error was (unfortunately I don't have the old source code > to make a diff on certain files), it is already corrected in the > up-to-the-minute version in the subversion system. > Try it out! > > Cheers, > Marcel > > > Charles Imbusch wrote: >> Hello Marcel, >> >> I also do experience the problem that the parser is skipping >> the even result numbers. I have not found a sufficient solution >> for that, so I gave up on parsing on a blast result file containing >> multiple results. Instead I splitted up the big fasta file into >> serveral ones, so that I just get one result for one fasta file. >> That works, even it's not the best solution for it. >> >> Let me know if you find another solution for that problem. >> >> Cheers, >> Charles >> >> > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l >