From pjotr.public14 at thebird.nl Thu Mar 11 12:41:38 2010 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 11 Mar 2010 18:41:38 +0100 Subject: [BioLib-dev] POD support Message-ID: <20100311174138.GA14929@thebird.nl> Creating Perl POD files from SWIG/Doxygen/Texi generated data is almost done. Attached an example for affyio. Note the methods are listed with their parameters. Getting there... I did a writeup on swig2pod here: http://biolib.open-bio.org/wiki/Biolib_Documentation_1.0 See also http://github.com/pjotrp/swig2doc Pj. -------------- next part -------------- An HTML attachment was scrubbed... URL: From rmb32 at cornell.edu Thu Mar 18 17:11:34 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Thu, 18 Mar 2010 14:11:34 -0700 Subject: [BioLib-dev] Google Summer of Code is *ON* for OBF projects! Message-ID: <4BA29706.8040606@cornell.edu> Hi all, Great news: Google announced today that the Open Bioinformatics Foundation has been accepted as a mentoring organization for this summer's Google Summer of Code! GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see GSoC 2010 FAQ at http://tinyurl.com/yzemdfo Student applications are due April 9, 2010 at 19:00 UTC. Students who are interested in participating should look at the OBF's GSoC page at http://open-bio.org/wiki/Google_Summer_of_Code, which lists project ideas, and who to contact about applying. For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on OBF wiki and on the relevant project's GSoC wiki page. Thanks to all who helped make OBF's application to GSoC a success, and let's have a great, productive summer of code! Rob Buels OBF GSoC 2010 Administrator From rmb32 at cornell.edu Fri Mar 26 03:44:09 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Fri, 26 Mar 2010 00:44:09 -0700 Subject: [BioLib-dev] GSoC mentors mailing list Message-ID: <4BAC65C9.307@cornell.edu> Hi all, If you have volunteered to be a possible GSoC mentor, and have not already been subscribed to the (mentors-only) gsoc-mentors mailing list, send me an email and I'll subscribe you. Rob Buels OBF GSoC 2010 Admin From luiz.irber at gmail.com Tue Mar 30 13:33:43 2010 From: luiz.irber at gmail.com (Luiz Irber) Date: Tue, 30 Mar 2010 14:33:43 -0300 Subject: [BioLib-dev] GSoC: Mapping JAVA libraries to Perl/Ruby/Python using Biolib+SWIG+JNI Message-ID: Hello, my name is Luiz Carlos Irber J?nior, currently a computer engineering undergrad (last semester) at Universidade Federal de S?o Carlos, Brazil. I have experience writing C bindings for Python with Cython (staff.get-e.org/?p=users/luizirber/python-eet.git) and C++ bindings too (but sadly it was on a company that didn't release the source). Looking for the available projects at OpenBio, I found this one, and started to research. I read the suggested link on the wiki, and http://www.swig.org/Doc1.3/Java.html too, but when I tried to find Fountain to actually try something... I couldn't find it. While searching I found that http://genetics.hpi.uni-hamburg.de/FOUNTAIN.html doesn't exist anymore, and apparently the source code isn't available anymore. What other Java libraries do you recommend for this project? Or where else can I find FOUNTAIN? Thanks, Luiz Irber From pjotr.public14 at thebird.nl Tue Mar 30 14:07:36 2010 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 30 Mar 2010 20:07:36 +0200 Subject: [BioLib-dev] GSoC: Mapping JAVA libraries to Perl/Ruby/Python using Biolib+SWIG+JNI In-Reply-To: References: Message-ID: <20100330180736.GA32545@thebird.nl> Hi Luiz, On Tue, Mar 30, 2010 at 02:33:43PM -0300, Luiz Irber wrote: > my name is Luiz Carlos Irber J?nior, currently a computer engineering > undergrad (last semester) at Universidade Federal de S?o Carlos, > Brazil. I have experience writing C bindings for Python with Cython > (staff.get-e.org/?p=users/luizirber/python-eet.git) and C++ bindings > too (but sadly it was on a company that didn't release the source). Meanwhile, Brazil has a great track record in OSS! Thank you for taking an interest in this challenging project. > Looking for the available projects at OpenBio, I found this one, and > started to research. I read the suggested link on the wiki, and > http://www.swig.org/Doc1.3/Java.html too, but when I tried to find > Fountain to actually try something... I couldn't find it. While > searching I found that > http://genetics.hpi.uni-hamburg.de/FOUNTAIN.html doesn't exist > anymore, and apparently the source code isn't available anymore. What > other Java libraries do you recommend for this project? Or where else > can I find FOUNTAIN? Hmmm. I guess we have to contact the authors for that. It looks like the Bioinformatics thing. After publication the authors disappear. But maybe it is temporary. For Biolib we are really interested in making JAVA available to SWIG over JNI. Any JAVA/Scala/Jython bioinformatics library could act as a proof of concept. As far as I am concerned you can bring up something completely different, as long as it covers some real JAVA-like functionality that would map SWIG through the JNI. If it is Fountain itself you are interested in I will contact the original authors and see if we can get it. What do you think? Pj. From luiz.irber at gmail.com Tue Mar 30 14:23:38 2010 From: luiz.irber at gmail.com (Luiz Irber) Date: Tue, 30 Mar 2010 15:23:38 -0300 Subject: [BioLib-dev] GSoC: Mapping JAVA libraries to Perl/Ruby/Python using Biolib+SWIG+JNI In-Reply-To: <9abd318e1003301122wa5a30ech92b76cc2b14bd234@mail.gmail.com> References: <20100330180736.GA32545@thebird.nl> <20100330181530.GA1131@thebird.nl> <9abd318e1003301122wa5a30ech92b76cc2b14bd234@mail.gmail.com> Message-ID: <9abd318e1003301123y5896a484k5dad9dd7ef18095a@mail.gmail.com> Hmm, let's get back to the list =] Luiz Irber ---------- Forwarded message ---------- From: Luiz Irber Date: Tue, Mar 30, 2010 at 3:22 PM Subject: Re: [BioLib-dev] GSoC: Mapping JAVA libraries to Perl/Ruby/Python using Biolib+SWIG+JNI To: Pjotr Prins On Tue, Mar 30, 2010 at 3:15 PM, Pjotr Prins wrote: > In fact the publication, I just noticed, is from 2001. How did I > manage that? I thought it was 2007. OK, let's forget Fountain. If you > see something you like we'll discuss. I can look for a different > example tomorrow, if required. I'm looking for other cool libraries, but I'm more interested in the SWIG/JNI mapping. The library is more for testing purposes. Is there any killer lib in BioJava, for example? We could try to map that, for example. Luiz Irber > > Pj. > > From pjotr.public14 at thebird.nl Wed Mar 31 14:13:39 2010 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 31 Mar 2010 20:13:39 +0200 Subject: [BioLib-dev] GSoC: Mapping JAVA libraries to Perl/Ruby/Python using Biolib+SWIG+JNI In-Reply-To: <9abd318e1003301413x58ba6e8ew515fa1d7a07f58bf@mail.gmail.com> References: <20100330180736.GA32545@thebird.nl> <9abd318e1003301413x58ba6e8ew515fa1d7a07f58bf@mail.gmail.com> Message-ID: <20100331181339.GA14080@thebird.nl> Hi Luiz, On Tue, Mar 30, 2010 at 06:13:02PM -0300, Luiz Irber wrote: > On Tue, Mar 30, 2010 at 3:07 PM, Pjotr Prins wrote: > > For Biolib we are really interested in making JAVA available to SWIG > > over JNI. Any JAVA/Scala/Jython bioinformatics library could act as a > > proof of concept. As far as I am concerned you can bring up something > > completely different, as long as it covers some real JAVA-like > > functionality that would map SWIG through the JNI. > > I think I found a good alternative: > > http://www.loci.wisc.edu/bio-formats > > They already have some solutions to interface non-Java code: > > http://www.loci.wisc.edu/bio-formats/interfacing-non-java-code Cool. Is there a language you would prefer to map to - Perl, Python, Ruby? A clear choice will allow us to get the relevant Bio* project interested in some functionality from JAVA. > And a C++ binding using Jace: > > https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/native/bf-cpp/ > > If they already have bindings working, what's the point? Why don't > just pick the C++ bindings and use them to expose methods to other > languages? Because Jace seems to be unmaintained (last release in > 2008), and it's not always a easy thing to map C++ to other languages > (at least in my experience). Yes. Correct. The C++ needs to be as simple as possible. > But, given that the bindings already exist, it could be wasted effort, > and we can find another one that don't have bindings yet. I don't > think that a pipeline like > > Java -> Jace -> C++ -> SWIG > > would perform well, but it can be tested. It is worth trying. Jace will (probably) generate a simple C++ interface, and it may be just the thing to do. If you make a plan I would start with spending time on assessing the combination with Jace. SWIG is very good a parsing C/C++ code. If Jace creates clean C++ code it may work well. In the next phase see if you can take Jace out of the equation. Especially if it does not deliver all the goods. It should be fairly easy to parse a standard JAVA class and convert it to something C-like that SWIG can accept. There should be other ways. Another strategy, after studying the way SWIG is implemented for JAVA - and other languages - you may be able to manipulate the JNI and query JAVA interactively for bindings (using reflection). After that write out the C headers for SWIG to parse. Another option to try would be using a grammar - and parse JAVA input files - there is a very good one written in JAVA named ANTLR http://www.antlr.org/. There are probably examples for parsing JAVA with ANTLR. I think the essence of this GSoC project is to study the different strategies, play around, and do a proof-of-concept finding the most elegant way of mapping Python (or Perl or R) against JAVA. So it is a project of pursuing different options and finding a route that will work for a lot of people. If you find an elegant way fame awaits you ;). It is important in your plan to create deliverables - in the sense of working pieces of code and tests. These will tell you (and us) how well a strategy is panning out. Challenging enough? Pj. From luiz.irber at gmail.com Wed Mar 31 17:25:34 2010 From: luiz.irber at gmail.com (Luiz Irber) Date: Wed, 31 Mar 2010 18:25:34 -0300 Subject: [BioLib-dev] GSoC: Mapping JAVA libraries to Perl/Ruby/Python using Biolib+SWIG+JNI In-Reply-To: <20100331181339.GA14080@thebird.nl> References: <20100330180736.GA32545@thebird.nl> <9abd318e1003301413x58ba6e8ew515fa1d7a07f58bf@mail.gmail.com> <20100331181339.GA14080@thebird.nl> Message-ID: On Wed, Mar 31, 2010 at 3:13 PM, Pjotr Prins wrote: > Cool. Is there a language you would prefer to map to - Perl, Python, > Ruby? A clear choice will allow us to get the relevant Bio* project > interested in some functionality from JAVA. I would go for Python, because it's the one I know better. > It is worth trying. Jace will (probably) generate a simple C++ > interface, and it may be just the thing to do. If you make a plan I > would start with spending time on assessing the combination with Jace. > > SWIG is very good a parsing C/C++ code. If Jace creates clean C++ code > it may work well. > > In the next phase see if you can take Jace out of the equation. > Especially if it does not deliver all the goods. I think it's a good goal for a first phase. And, to test it, we can generate Java bindings via SWIG for the Jace C++ generated bindings in Java, to see if it works =D > It should be fairly easy to parse a standard JAVA class and convert it > to something C-like that SWIG can accept. There should be other ways. I was reading the docs on SWIG internals, and they have a basic object system called DOH. We can map Java types and objects to them at first, and see how it goes. > Another strategy, after studying the way SWIG is implemented for JAVA - > and other languages - you may be able to manipulate the JNI and query > JAVA interactively for bindings (using reflection). After that write > out the C headers for SWIG to parse. > > Another option to try would be using a grammar - and parse JAVA input > files - there is a very good one written in JAVA named ANTLR > http://www.antlr.org/. There are probably examples for parsing JAVA > with ANTLR. Pretty good options too. I was thinking on going the parser way, and use the already existing SWIG structure, but we can try ANTLR too. > I think the essence of this GSoC project is to study the different > strategies, play around, and do a proof-of-concept finding the most > elegant way of mapping Python (or Perl or R) against JAVA. So it is a > project of pursuing different options and finding a route that will > work for a lot of people. If you find an elegant way fame awaits you > ;). Yes, I think a complete solution would take more time than GSoC provide, but a good proof-of-concept is definitely doable. Gonna start to write the GSoC application. > It is important in your plan to create deliverables - in the sense of > working pieces of code and tests. These will tell you (and us) how > well a strategy is panning out. > > Challenging enough? Challenging and exciting =D Luiz Irber > > Pj. > From pjotr.public14 at thebird.nl Thu Mar 11 17:41:38 2010 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 11 Mar 2010 18:41:38 +0100 Subject: [BioLib-dev] POD support Message-ID: <20100311174138.GA14929@thebird.nl> Creating Perl POD files from SWIG/Doxygen/Texi generated data is almost done. Attached an example for affyio. Note the methods are listed with their parameters. Getting there... I did a writeup on swig2pod here: http://biolib.open-bio.org/wiki/Biolib_Documentation_1.0 See also http://github.com/pjotrp/swig2doc Pj. -------------- next part -------------- An HTML attachment was scrubbed... URL: From rmb32 at cornell.edu Thu Mar 18 21:11:34 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Thu, 18 Mar 2010 14:11:34 -0700 Subject: [BioLib-dev] Google Summer of Code is *ON* for OBF projects! Message-ID: <4BA29706.8040606@cornell.edu> Hi all, Great news: Google announced today that the Open Bioinformatics Foundation has been accepted as a mentoring organization for this summer's Google Summer of Code! GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see GSoC 2010 FAQ at http://tinyurl.com/yzemdfo Student applications are due April 9, 2010 at 19:00 UTC. Students who are interested in participating should look at the OBF's GSoC page at http://open-bio.org/wiki/Google_Summer_of_Code, which lists project ideas, and who to contact about applying. For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on OBF wiki and on the relevant project's GSoC wiki page. Thanks to all who helped make OBF's application to GSoC a success, and let's have a great, productive summer of code! Rob Buels OBF GSoC 2010 Administrator From rmb32 at cornell.edu Fri Mar 26 07:44:09 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Fri, 26 Mar 2010 00:44:09 -0700 Subject: [BioLib-dev] GSoC mentors mailing list Message-ID: <4BAC65C9.307@cornell.edu> Hi all, If you have volunteered to be a possible GSoC mentor, and have not already been subscribed to the (mentors-only) gsoc-mentors mailing list, send me an email and I'll subscribe you. Rob Buels OBF GSoC 2010 Admin From luiz.irber at gmail.com Tue Mar 30 17:33:43 2010 From: luiz.irber at gmail.com (Luiz Irber) Date: Tue, 30 Mar 2010 14:33:43 -0300 Subject: [BioLib-dev] GSoC: Mapping JAVA libraries to Perl/Ruby/Python using Biolib+SWIG+JNI Message-ID: Hello, my name is Luiz Carlos Irber J?nior, currently a computer engineering undergrad (last semester) at Universidade Federal de S?o Carlos, Brazil. I have experience writing C bindings for Python with Cython (staff.get-e.org/?p=users/luizirber/python-eet.git) and C++ bindings too (but sadly it was on a company that didn't release the source). Looking for the available projects at OpenBio, I found this one, and started to research. I read the suggested link on the wiki, and http://www.swig.org/Doc1.3/Java.html too, but when I tried to find Fountain to actually try something... I couldn't find it. While searching I found that http://genetics.hpi.uni-hamburg.de/FOUNTAIN.html doesn't exist anymore, and apparently the source code isn't available anymore. What other Java libraries do you recommend for this project? Or where else can I find FOUNTAIN? Thanks, Luiz Irber From pjotr.public14 at thebird.nl Tue Mar 30 18:07:36 2010 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 30 Mar 2010 20:07:36 +0200 Subject: [BioLib-dev] GSoC: Mapping JAVA libraries to Perl/Ruby/Python using Biolib+SWIG+JNI In-Reply-To: References: Message-ID: <20100330180736.GA32545@thebird.nl> Hi Luiz, On Tue, Mar 30, 2010 at 02:33:43PM -0300, Luiz Irber wrote: > my name is Luiz Carlos Irber J?nior, currently a computer engineering > undergrad (last semester) at Universidade Federal de S?o Carlos, > Brazil. I have experience writing C bindings for Python with Cython > (staff.get-e.org/?p=users/luizirber/python-eet.git) and C++ bindings > too (but sadly it was on a company that didn't release the source). Meanwhile, Brazil has a great track record in OSS! Thank you for taking an interest in this challenging project. > Looking for the available projects at OpenBio, I found this one, and > started to research. I read the suggested link on the wiki, and > http://www.swig.org/Doc1.3/Java.html too, but when I tried to find > Fountain to actually try something... I couldn't find it. While > searching I found that > http://genetics.hpi.uni-hamburg.de/FOUNTAIN.html doesn't exist > anymore, and apparently the source code isn't available anymore. What > other Java libraries do you recommend for this project? Or where else > can I find FOUNTAIN? Hmmm. I guess we have to contact the authors for that. It looks like the Bioinformatics thing. After publication the authors disappear. But maybe it is temporary. For Biolib we are really interested in making JAVA available to SWIG over JNI. Any JAVA/Scala/Jython bioinformatics library could act as a proof of concept. As far as I am concerned you can bring up something completely different, as long as it covers some real JAVA-like functionality that would map SWIG through the JNI. If it is Fountain itself you are interested in I will contact the original authors and see if we can get it. What do you think? Pj. From luiz.irber at gmail.com Tue Mar 30 18:23:38 2010 From: luiz.irber at gmail.com (Luiz Irber) Date: Tue, 30 Mar 2010 15:23:38 -0300 Subject: [BioLib-dev] GSoC: Mapping JAVA libraries to Perl/Ruby/Python using Biolib+SWIG+JNI In-Reply-To: <9abd318e1003301122wa5a30ech92b76cc2b14bd234@mail.gmail.com> References: <20100330180736.GA32545@thebird.nl> <20100330181530.GA1131@thebird.nl> <9abd318e1003301122wa5a30ech92b76cc2b14bd234@mail.gmail.com> Message-ID: <9abd318e1003301123y5896a484k5dad9dd7ef18095a@mail.gmail.com> Hmm, let's get back to the list =] Luiz Irber ---------- Forwarded message ---------- From: Luiz Irber Date: Tue, Mar 30, 2010 at 3:22 PM Subject: Re: [BioLib-dev] GSoC: Mapping JAVA libraries to Perl/Ruby/Python using Biolib+SWIG+JNI To: Pjotr Prins On Tue, Mar 30, 2010 at 3:15 PM, Pjotr Prins wrote: > In fact the publication, I just noticed, is from 2001. How did I > manage that? I thought it was 2007. OK, let's forget Fountain. If you > see something you like we'll discuss. I can look for a different > example tomorrow, if required. I'm looking for other cool libraries, but I'm more interested in the SWIG/JNI mapping. The library is more for testing purposes. Is there any killer lib in BioJava, for example? We could try to map that, for example. Luiz Irber > > Pj. > > From pjotr.public14 at thebird.nl Wed Mar 31 18:13:39 2010 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 31 Mar 2010 20:13:39 +0200 Subject: [BioLib-dev] GSoC: Mapping JAVA libraries to Perl/Ruby/Python using Biolib+SWIG+JNI In-Reply-To: <9abd318e1003301413x58ba6e8ew515fa1d7a07f58bf@mail.gmail.com> References: <20100330180736.GA32545@thebird.nl> <9abd318e1003301413x58ba6e8ew515fa1d7a07f58bf@mail.gmail.com> Message-ID: <20100331181339.GA14080@thebird.nl> Hi Luiz, On Tue, Mar 30, 2010 at 06:13:02PM -0300, Luiz Irber wrote: > On Tue, Mar 30, 2010 at 3:07 PM, Pjotr Prins wrote: > > For Biolib we are really interested in making JAVA available to SWIG > > over JNI. Any JAVA/Scala/Jython bioinformatics library could act as a > > proof of concept. As far as I am concerned you can bring up something > > completely different, as long as it covers some real JAVA-like > > functionality that would map SWIG through the JNI. > > I think I found a good alternative: > > http://www.loci.wisc.edu/bio-formats > > They already have some solutions to interface non-Java code: > > http://www.loci.wisc.edu/bio-formats/interfacing-non-java-code Cool. Is there a language you would prefer to map to - Perl, Python, Ruby? A clear choice will allow us to get the relevant Bio* project interested in some functionality from JAVA. > And a C++ binding using Jace: > > https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/native/bf-cpp/ > > If they already have bindings working, what's the point? Why don't > just pick the C++ bindings and use them to expose methods to other > languages? Because Jace seems to be unmaintained (last release in > 2008), and it's not always a easy thing to map C++ to other languages > (at least in my experience). Yes. Correct. The C++ needs to be as simple as possible. > But, given that the bindings already exist, it could be wasted effort, > and we can find another one that don't have bindings yet. I don't > think that a pipeline like > > Java -> Jace -> C++ -> SWIG > > would perform well, but it can be tested. It is worth trying. Jace will (probably) generate a simple C++ interface, and it may be just the thing to do. If you make a plan I would start with spending time on assessing the combination with Jace. SWIG is very good a parsing C/C++ code. If Jace creates clean C++ code it may work well. In the next phase see if you can take Jace out of the equation. Especially if it does not deliver all the goods. It should be fairly easy to parse a standard JAVA class and convert it to something C-like that SWIG can accept. There should be other ways. Another strategy, after studying the way SWIG is implemented for JAVA - and other languages - you may be able to manipulate the JNI and query JAVA interactively for bindings (using reflection). After that write out the C headers for SWIG to parse. Another option to try would be using a grammar - and parse JAVA input files - there is a very good one written in JAVA named ANTLR http://www.antlr.org/. There are probably examples for parsing JAVA with ANTLR. I think the essence of this GSoC project is to study the different strategies, play around, and do a proof-of-concept finding the most elegant way of mapping Python (or Perl or R) against JAVA. So it is a project of pursuing different options and finding a route that will work for a lot of people. If you find an elegant way fame awaits you ;). It is important in your plan to create deliverables - in the sense of working pieces of code and tests. These will tell you (and us) how well a strategy is panning out. Challenging enough? Pj. From luiz.irber at gmail.com Wed Mar 31 21:25:34 2010 From: luiz.irber at gmail.com (Luiz Irber) Date: Wed, 31 Mar 2010 18:25:34 -0300 Subject: [BioLib-dev] GSoC: Mapping JAVA libraries to Perl/Ruby/Python using Biolib+SWIG+JNI In-Reply-To: <20100331181339.GA14080@thebird.nl> References: <20100330180736.GA32545@thebird.nl> <9abd318e1003301413x58ba6e8ew515fa1d7a07f58bf@mail.gmail.com> <20100331181339.GA14080@thebird.nl> Message-ID: On Wed, Mar 31, 2010 at 3:13 PM, Pjotr Prins wrote: > Cool. Is there a language you would prefer to map to - Perl, Python, > Ruby? A clear choice will allow us to get the relevant Bio* project > interested in some functionality from JAVA. I would go for Python, because it's the one I know better. > It is worth trying. Jace will (probably) generate a simple C++ > interface, and it may be just the thing to do. If you make a plan I > would start with spending time on assessing the combination with Jace. > > SWIG is very good a parsing C/C++ code. If Jace creates clean C++ code > it may work well. > > In the next phase see if you can take Jace out of the equation. > Especially if it does not deliver all the goods. I think it's a good goal for a first phase. And, to test it, we can generate Java bindings via SWIG for the Jace C++ generated bindings in Java, to see if it works =D > It should be fairly easy to parse a standard JAVA class and convert it > to something C-like that SWIG can accept. There should be other ways. I was reading the docs on SWIG internals, and they have a basic object system called DOH. We can map Java types and objects to them at first, and see how it goes. > Another strategy, after studying the way SWIG is implemented for JAVA - > and other languages - you may be able to manipulate the JNI and query > JAVA interactively for bindings (using reflection). After that write > out the C headers for SWIG to parse. > > Another option to try would be using a grammar - and parse JAVA input > files - there is a very good one written in JAVA named ANTLR > http://www.antlr.org/. There are probably examples for parsing JAVA > with ANTLR. Pretty good options too. I was thinking on going the parser way, and use the already existing SWIG structure, but we can try ANTLR too. > I think the essence of this GSoC project is to study the different > strategies, play around, and do a proof-of-concept finding the most > elegant way of mapping Python (or Perl or R) against JAVA. So it is a > project of pursuing different options and finding a route that will > work for a lot of people. If you find an elegant way fame awaits you > ;). Yes, I think a complete solution would take more time than GSoC provide, but a good proof-of-concept is definitely doable. Gonna start to write the GSoC application. > It is important in your plan to create deliverables - in the sense of > working pieces of code and tests. These will tell you (and us) how > well a strategy is panning out. > > Challenging enough? Challenging and exciting =D Luiz Irber > > Pj. >