From radomir.adamek at hotmail.com Wed Feb 6 02:03:30 2013 From: radomir.adamek at hotmail.com (Radomir) Date: Tue, 5 Feb 2013 23:03:30 -0800 (PST) Subject: [Biojava-l] BioJava, oracle problem with jdk Message-ID: <34984653.post@talk.nabble.com> Hello, i`m trying to apply my project with oracle and biojava. I`m trying to make a database for pairwise alignment ( FATCAT or CE ). These algorithms are in biojava3+ packages. When i`m loading jar`s to mine database i got error ( oracle is running on 1.5 jdk and biojava 3 is compiled on 1.6, there are no chances to upgrade jdk on oracle ).. I find on biojava wiki that version 3.0 of biojava is running on 1.5+ but when i loaded these version to my database there was the same error. Here is my question - is there any chances to get biojava 3 compiled with jdk 1.5 ? ? Sorry for my english -- View this message in context: http://old.nabble.com/BioJava%2C-oracle-problem-with-jdk-tp34984653p34984653.html Sent from the BioJava mailing list archive at Nabble.com. From amr_alhossary at hotmail.com Wed Feb 6 02:13:55 2013 From: amr_alhossary at hotmail.com (Amr AL-HOSSARY) Date: Wed, 6 Feb 2013 15:13:55 +0800 Subject: [Biojava-l] BioJava, oracle problem with jdk In-Reply-To: <34984653.post@talk.nabble.com> References: <34984653.post@talk.nabble.com> Message-ID: Greetings Radomir, If you are using Eclipse, you can obtain a checkout copy of the source code, compile it on Java 6, and in the compiler settings, search for an option to generate Java 5 compatible byte code, generate jars, and use them. You may need to compile them yourself (not as Maven projects), but I am not sure of that. Best Regards, Amr AL-HOSSARY Amr Ali AL-HOSSARY | Ph.D. Student | International PhD program in Computational Biology and Bioinformatics | School of Computer Engineering | Nanyang Technological University | Singapore | Email: amra0001 at e.ntu.edu.sg | > Date: Tue, 5 Feb 2013 23:03:30 -0800 > From: radomir.adamek at hotmail.com > To: biojava-l at lists.open-bio.org > Subject: [Biojava-l] BioJava, oracle problem with jdk > > > Hello, i`m trying to apply my project with oracle and biojava. I`m trying to > make a database for pairwise alignment ( FATCAT or CE ). These algorithms > are in biojava3+ packages. When i`m loading jar`s to mine database i got > error ( oracle is running on 1.5 jdk and biojava 3 is compiled on 1.6, there > are no chances to upgrade jdk on oracle ).. I find on biojava wiki that > version 3.0 of biojava is running on 1.5+ but when i loaded these version to > my database there was the same error. Here is my question - is there any > chances to get biojava 3 compiled with jdk 1.5 ? ? Sorry for my english > -- > View this message in context: http://old.nabble.com/BioJava%2C-oracle-problem-with-jdk-tp34984653p34984653.html > Sent from the BioJava mailing list archive at Nabble.com. > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From darnells at dnastar.com Wed Feb 6 11:24:55 2013 From: darnells at dnastar.com (Steve Darnell) Date: Wed, 6 Feb 2013 16:24:55 +0000 Subject: [Biojava-l] BioJava, oracle problem with jdk In-Reply-To: <34984653.post@talk.nabble.com> References: <34984653.post@talk.nabble.com> Message-ID: Hi Radomir, I expect you must be using a Mac with a PPC or 32-bit Intel CPU. Apple Java 6 is not available for PPC architecture nor 32-bit Intel machines running OS X 10.5 or lower. Java 6 is available on Windows XP/Vista/7, Linux, and Mac OS X 10.5 (64-bit only)/10.6+. If you must use Java 5, your options are: * Build BioJava yourself (as Amr suggested): http://biojava.org/wiki/Get_source, http://biojava.org/wiki/BioJava3_eclipse * Try SoyLatte: http://landonf.bikemonkey.org/static/soylatte/, Java 6 port for Mac OS X 10.4, 10.5 (Intel) If you go the SoyLatte route, be prepared to pray for it to work. It is several years old. If it were me, I'd update my Mac to 10.6 then hope the mainboard doesn't fail. I'm not a huge fan of 10.7+, but I'll be forced to go there eventually. ~Steve -----Original Message----- From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Radomir Sent: Wednesday, February 06, 2013 1:04 AM To: biojava-l at lists.open-bio.org Subject: [Biojava-l] BioJava, oracle problem with jdk Hello, i`m trying to apply my project with oracle and biojava. I`m trying to make a database for pairwise alignment ( FATCAT or CE ). These algorithms are in biojava3+ packages. When i`m loading jar`s to mine database i got error ( oracle is running on 1.5 jdk and biojava 3 is compiled on 1.6, there are no chances to upgrade jdk on oracle ).. I find on biojava wiki that version 3.0 of biojava is running on 1.5+ but when i loaded these version to my database there was the same error. Here is my question - is there any chances to get biojava 3 compiled with jdk 1.5 ? ? Sorry for my english -- View this message in context: http://old.nabble.com/BioJava%2C-oracle-problem-with-jdk-tp34984653p34984653.html Sent from the BioJava mailing list archive at Nabble.com. _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From andreas at sdsc.edu Wed Feb 6 11:54:37 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Wed, 6 Feb 2013 08:54:37 -0800 Subject: [Biojava-l] preparations for Google Summer of Code Message-ID: Hi, Google has not released yet if they will sponsor another Google Summer of Code this year, but we should still try to prepare, so we are ready if/when the announcement comes out. Any project ideas that we want people to work on this summer? I stated a new wiki page for this at http://biojava.org/wiki/Google_Summer_of_Code_2013 Andreas From pwrose at ucsd.edu Mon Feb 11 13:12:56 2013 From: pwrose at ucsd.edu (Peter Rose) Date: Mon, 11 Feb 2013 18:12:56 +0000 Subject: [Biojava-l] [Job] Take the RCSB PDB site to the next level Message-ID: The RCSB PDB at the University of California, San Diego is looking for a talented Java Developer/Lead Web Architect: The RCSB Protein Data Bank (http://www.rcsb.org) is one of the premier biological databases worldwide with a growing user base of currently about 300,000 unique users per month. We constantly strive to make our site perform better, make it look nicer and offer new and exciting scientific applications to our diverse user base that includes scientists, students, teachers and other researchers. We offer a flexible work environment in a dynamic team. We offer the challenge to take the RCSB PDB web site to the next level. For this we are looking for a lead architect and Java web developer. You will provide expertise and leadership in enhancing the data warehouse and middle layer of the PDB website's 3-tier architecture by working with a team of scientists and software developers. Translate new and emergent requirements for the website into strategic plans to select the best web technologies and architectures for the PDB site. Author functional requirements, technical design documents, and project plans. Incorporate advanced scientific query and analysis tools, and novel representation of results in the web application. Provide technical leadership, guidance, and training on new web technologies to RCSB team and provide high level and implementation level suggestions for improving design, coding, and testing methodologies. Develop best project management and software engineering practices. Our technology stack includes Java, MySQL, Hibernate, and Memcached. UC San Diego is an Equal Opportunity / Staff Affirmative Action Employer that values a diverse workforce and provides reasonable accommodations to people with disabilities. We offer a generous benefits package: http://www.sdsc.edu/about/Careers.html. Please apply online at: http://jobs.ucsd.edu/bulletin/job.aspx?cat=information&sortby=post&jobnum_in=64091 QUALIFICATIONS * BS Degree in Computer Science or comparable combination of education and experience with considerable focus in Java software development. * Established demonstrated work experience in the role of an architect and developer on medium to large size database-driven web applications using Java technology and standards. * Advanced experience with database design, Structured Query Language and RDBMS's such as MySQL, and object-relational mappings. Expertise in web application server (i.e., Tomcat) administration, configuration, trouble shooting, and performance tuning. * Established expertise in software life cycle methodologies. Experience with build tools such as Maven and Ant, and continuous integration systems such as Cruise Control. Experience with project tracking tools such as Jira . ________________________________________________ Peter Rose, Ph.D. Scientific Lead RCSB Protein Data Bank (http://www.rcsb.org) San Diego Supercomputer Center (SDSC) and Skaggs School of Pharmacy and Pharmaceutical Sciences Pharmaceutical Sciences Building University of California San Diego 9500 Gilman Drive, Mailcode 0743 La Jolla, CA 92093-0743 Email: pwrose at ucsd.edu Voice: (858) 822-5497 Fax: (858) 822-0873 From andreas at sdsc.edu Mon Feb 11 14:18:52 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 11 Feb 2013 11:18:52 -0800 Subject: [Biojava-l] Fwd: [GSoC Mentors Announce] Google Summer of Code 2013 In-Reply-To: References: Message-ID: Hi, Google summer of code 2013 has been announced... Anybody interested in mentoring, or suggesting projects for this year? Andreas ---------- Forwarded message ---------- From: Carol Smith Date: Mon, Feb 11, 2013 at 11:02 AM Subject: [GSoC Mentors Announce] Google Summer of Code 2013 To: gsoc-mentors-announce at googlegroups.com Hi GSoC mentors and org admins, We've announced that we're doing Google Summer of Code 2013 [1]. Yay! If you would like to help spread the word about GSoC, we have presentations [2], logos [3], and flyers [4] for you to use. Please host meetups, tell your friends and colleagues about the program, go to conferences, talk to people about the program, and just generally do all the awesome word-of-mouth stuff you do every year to promote the program. The GSoC calendar, FAQ, and events timeline have all been updated with this year's important dates, so please refer to those for the milestones for this year's program. NB: the normal timeline for the program has been modified for this year. You'll probably want to examine the dates closely to make sure you know when important things are happening. Please consider translating the presentations and/or flyers into your native language and submitting them directly to me to post on the wiki. Localization for our material is integral to reaching the widest possible audience around the world. If you decide to translate a flyer, please fill out our form to request a thank you gift for your effort. [5] If you decide to host a meetup, please email me to let me know the date, time, and location so I can put it on the GSoC calendar. Also, remember to take pictures at your meetup and write up a blog post for our blog using our provided template for formatting [6]. If you need promotional items for your attendees, please fill out our form [7] to request some; we're happy to send some along. We can provide up to about 25 pens, notebooks, or stickers and/or a few t-shirts. Please keep in mind, though, that shipping restrictions and timeline vary country-to-country; request items early to make sure they get there on time! If you have questions about hosting meetups, please see the section in our FAQ [8]. Please also consider applying to participate as an organization again this year or maybe joining as a mentor for your favorite organization if they are selected this year. We rely on you for your help for the success of this program, so thank you in advance for all the work you do! [1] - http://google-opensource.blogspot.com/2013/02/flip-bits-not-burgers-google-summer-of.html [2] - http://code.google.com/p/google-summer-of-code/wiki/ProgramPresentations [3] - http://code.google.com/p/google-summer-of-code/wiki/GsocLogos [4] - http://code.google.com/p/google-summer-of-code/wiki/GsocFlyers [5] - http://goo.gl/gEHDO [6] - http://goo.gl/wbZrt [7] - http://goo.gl/0BsR8 [8] - http://goo.gl/2NGfp Cheers, Carol -- You received this message because you are subscribed to the Google Groups "Google Summer of Code Mentors Announce List" group. To unsubscribe from this group and stop receiving emails from it, send an email to gsoc-mentors-announce+unsubscribe at googlegroups.com. Visit this group at http://groups.google.com/group/gsoc-mentors-announce?hl=en-US. For more options, visit https://groups.google.com/groups/opt_out. From heuermh at gmail.com Mon Feb 11 16:33:59 2013 From: heuermh at gmail.com (Michael Heuer) Date: Mon, 11 Feb 2013 15:33:59 -0600 Subject: [Biojava-l] 2013 BOSC/Broad Interoperability Hackathon + BOSC Codefest Message-ID: All, Just wanted to announce to and/or remind folks of two upcoming BOSC and Biojava-related events: April 7-8, 2013: BOSC/Broad Interoperability Hackathon, Cambridge, MA http://www.broadinstitute.org/events/interoperability-hackathon-2013/home July 17-18, 2013: Codefest 2013, Berlin http://www.open-bio.org/wiki/Codefest_2013 michael From saidi34 at hushmail.com Tue Feb 12 12:39:07 2013 From: saidi34 at hushmail.com (saidi34 at hushmail.com) Date: Tue, 12 Feb 2013 12:39:07 -0500 Subject: [Biojava-l] =?utf-8?q?A_Ph=2ED=2E_Student=E2=80=99s_CRY_for_Help?= Message-ID: <20130212173907.6C263E6726@smtp.hushmail.com> A Ph.D. Student?s CRY for Help To: Prof. Hamid Arabnia, WORLDCOMP Coordinator, Professor of Computer Science, University of Georgia, USA Prof. Hamid Arabnia, I am a student from Africa and I am in the final stages of my Ph.D. work. I have a journal paper in ACM and a conference paper in WORLDCOMP. As per my university policy, I am required to have at least two research papers in peer-reviewed (refereed) international conferences or journals before I submit my synopsis/dissertation. While everything was fine, recently, WORLDCOMP was declared as a bogus conference with evidences and endorsements from scientists: https://sites.google.com/site/worlddump1 Also see http://worldcomp-fake-bogus.blogspot.com Now, my university officials have stopped me from submitting the dissertation stating that WORLDCOMP is not peer-reviewed due to the evidences in these websites. They said that WORLDCOMP is completely fake and that?s why you have not responded to the open challenge at https://sites.google.com/site/dumpconf or https://sites.google.com/site/moneycomp1 I sent many emails to you requesting to respond to the open challenge and prove that WORLDCOMP is not fake so that I can show your response to my university officials and convince them and submit my dissertation. I also asked you to email me the reviews for my paper (I never received them, although your acceptance email stated that the paper was reviewed by two experts) but you are not responding. Recall that when I met you in WORLDCOMP, you offered me a reference letter and invited me to organize a session in the next conference and promised free registration for my next paper if I get at least five registered papers fr om others. Now I am shocked with your silence. I am clueless on what to do as I will forfeit my student status unless I submit the dissertation soon. I am facing humiliation here. I was attracted by the keynote speakers, sponsors, tutorials, and University of Georgia name at WORLDCOMP website. Now I feel that I made a very critical mistake by submitting to WORLDCOMP. As the last resort, I am posting to this mailing list/forum (where WORLDCOMP details were published in the past I think) so that you understand the seriousness. I once again ask you to provide a detailed response at WORLDCOMP?s website and prove that it is not a fake (and also email me my paper reviews). I request you to focus on this issue than organizing the next conference (and create more victims like me). I hope you still have moral values. My elderly parents are dependent on me and I am crying for help. I openly beg your response! Respectfully, Saidi (this is my nickname and I am using it to avoid further humiliation. I know that you will easily identify me from this nickname and from my background mentioned above). To the forum/list owner: please understand my situation and publish this message and it will help other researchers to be more careful while choosing a conference. To the members: please help me getting a response from Prof. Arabnia. From andreas at sdsc.edu Wed Feb 13 19:10:29 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Wed, 13 Feb 2013 16:10:29 -0800 Subject: [Biojava-l] BioJava SVN moving to github Message-ID: Hi, as we have discussed several times over the last months, the time has come to migrate the BioJava SVN repository to github. I want to thank Spencer Bliven who has volunteered to be in charge of this migration and who will guide us through this process. Thanks, Spencer! Andreas From hlapp at drycafe.net Wed Feb 13 23:21:54 2013 From: hlapp at drycafe.net (Hilmar Lapp) Date: Wed, 13 Feb 2013 23:21:54 -0500 Subject: [Biojava-l] BioJava SVN moving to github In-Reply-To: References: Message-ID: On Feb 13, 2013, at 7:10 PM, Andreas Prlic wrote: > as we have discussed several times over the last months, the time has come > to migrate the BioJava SVN repository to github. Great! -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From jprocter at compbio.dundee.ac.uk Fri Feb 15 09:50:35 2013 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Fri, 15 Feb 2013 14:50:35 +0000 Subject: [Biojava-l] BioJava SVN moving to github In-Reply-To: References: Message-ID: <511E4B3B.1050909@compbio.dundee.ac.uk> On Thu Feb 14 04:21:54 2013, Hilmar Lapp wrote: > > On Feb 13, 2013, at 7:10 PM, Andreas Prlic wrote: > >> as we have discussed several times over the last months, the time has come >> to migrate the BioJava SVN repository to github. May the g-force be with you, Spencer! ..Jim. From jjramirez at estudiantes.uci.cu Sun Feb 17 22:24:44 2013 From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=) Date: Sun, 17 Feb 2013 22:24:44 -0500 (EST) Subject: [Biojava-l] Reading SCF files In-Reply-To: Message-ID: <9b0b495e-a4c6-4e0c-923d-791ae836ae51@ucimail4.uci.cu> Hello, I need to read an SCF file using BioJava to finally show the chromatogram, but I don't know what version of BioJava to use Thanks for your time -- There is no knowledge, that is not power From andreas at sdsc.edu Sun Feb 17 23:25:32 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Sun, 17 Feb 2013 20:25:32 -0800 Subject: [Biojava-l] Reading SCF files In-Reply-To: <9b0b495e-a4c6-4e0c-923d-791ae836ae51@ucimail4.uci.cu> References: <9b0b495e-a4c6-4e0c-923d-791ae836ae51@ucimail4.uci.cu> Message-ID: Hi Janier, that is part of BioJava 1... Andreas On Sun, Feb 17, 2013 at 7:24 PM, Janier J. Ram?rez < jjramirez at estudiantes.uci.cu> wrote: > Hello, I need to read an SCF file using BioJava to finally show the > chromatogram, but I don't know what version of BioJava to use > > Thanks for your time > -- > There is no knowledge, that is not power > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From jjramirez at estudiantes.uci.cu Mon Feb 18 00:09:08 2013 From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=) Date: Mon, 18 Feb 2013 00:09:08 -0500 (EST) Subject: [Biojava-l] Reading SCF files In-Reply-To: <9b0b495e-a4c6-4e0c-923d-791ae836ae51@ucimail4.uci.cu> Message-ID: Yes that's ok, Now I need an example of how given the path of the scf file, get the secuence, to them parse it to fasta, or if I can do it directly from scf to fasta. Thanks for your time From nickengland at gmail.com Mon Feb 18 05:13:12 2013 From: nickengland at gmail.com (Nick England) Date: Mon, 18 Feb 2013 10:13:12 +0000 Subject: [Biojava-l] Reading SCF files In-Reply-To: References: <9b0b495e-a4c6-4e0c-923d-791ae836ae51@ucimail4.uci.cu> Message-ID: Janier, Here is a snippet which should read in SCF files for you, you will have to have BioJava 1.0 for this to work. File file = new File(String "your path here"); InputStream stream = new FileInputStream(file); Chromatogram scf= ChromatogramFactory.create(stream); stream.close(); Alignment data = scf.getBaseCalls(); String seq=data.symbolListForLabel("dna").seqString(); Cheers, Nick On 18 February 2013 05:09, Janier J. Ram?rez wrote: > Yes that's ok, Now I need an example of how given the path of the scf > file, get the secuence, to them parse it to fasta, or if I can do it > directly from scf to fasta. > > Thanks for your time > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From radomir.adamek at hotmail.com Mon Feb 18 06:46:03 2013 From: radomir.adamek at hotmail.com (Radomir) Date: Mon, 18 Feb 2013 03:46:03 -0800 (PST) Subject: [Biojava-l] BioJava, oracle problem with jdk In-Reply-To: <34984653.post@talk.nabble.com> References: <34984653.post@talk.nabble.com> Message-ID: <35036008.post@talk.nabble.com> Hi, thanks for reply. I`m having more problems with "recompiling" from 1.6 to 1.5. I have done everything like u told me. When i`m trying to clean install with maven compiler i got error with version. Can somebody tell me its possible to compile biojava 3 with 1.5 jdk? I don`t have idea how to do that and its very important for me ( my final project on my studies ). Here is a part of error from compiler: [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.5.1:compile (default-compile) on project biojava3-structure: Compilation failure [ERROR] C:\Users\radamek\workspace\maven.1361187141685\biojava\biojava3-structure\src\main\java\org\biojava\bio\structure\Chain.java:[28,-1] cannot access org.biojava3.core.sequence.template.Sequence [ERROR] bad class file: C:\Users\radamek\.m2\repository\org\biojava\biojava3-core\3.0.6-SNAPSHOT\biojava3-core-3.0.6-SNAPSHOT.jar(org/biojava3/core/sequence/template/Sequence.class) [ERROR] class file has wrong version 50.0, should be 49.0 Radomir wrote: > > Hello, i`m trying to apply my project with oracle and biojava. I`m trying > to make a database for pairwise alignment ( FATCAT or CE ). These > algorithms are in biojava3+ packages. When i`m loading jar`s to mine > database i got error ( oracle is running on 1.5 jdk and biojava 3 is > compiled on 1.6, there are no chances to upgrade jdk on oracle ).. I find > on biojava wiki that version 3.0 of biojava is running on 1.5+ but when i > loaded these version to my database there was the same error. Here is my > question - is there any chances to get biojava 3 compiled with jdk 1.5 ? ? > Sorry for my english > -- View this message in context: http://old.nabble.com/BioJava%2C-oracle-problem-with-jdk-tp34984653p35036008.html Sent from the BioJava mailing list archive at Nabble.com. From radomir.adamek at hotmail.com Tue Feb 19 03:59:19 2013 From: radomir.adamek at hotmail.com (Radomir) Date: Tue, 19 Feb 2013 00:59:19 -0800 (PST) Subject: [Biojava-l] BioJava, oracle problem with jdk In-Reply-To: <35036008.post@talk.nabble.com> References: <34984653.post@talk.nabble.com> <35036008.post@talk.nabble.com> Message-ID: <35040215.post@talk.nabble.com> Hello, sorry for spam. I solved the last error but i got new one. I can compile core package to version 1.5 jdk but when i try to compile phylo package i got error like that: [INFO] biojava ........................................... SUCCESS [0.748s] [INFO] biojava3-core ..................................... SUCCESS [7.076s] [INFO] biojava3-phylo .................................... FAILURE [0.321s] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.5.1:compile (default-compile) on project biojava3-phylo: Compilation failure [ERROR] Failure executing javac, but could not parse the error: [ERROR] javac: invalid flag: -s [ERROR] Usage: javac can anyone help me?? i don`t have idea what i`m making wrong. Radomir wrote: > > Hi, thanks for reply. I`m having more problems with "recompiling" from 1.6 > to 1.5. I have done everything like u told me. When i`m trying to clean > install with maven compiler i got error with version. Can somebody tell me > its possible to compile biojava 3 with 1.5 jdk? I don`t have idea how to > do that and its very important for me ( my final project on my studies ). > Here is a part of error from compiler: > > [ERROR] Failed to execute goal > org.apache.maven.plugins:maven-compiler-plugin:2.5.1:compile > (default-compile) on project biojava3-structure: Compilation failure > [ERROR] > C:\Users\radamek\workspace\maven.1361187141685\biojava\biojava3-structure\src\main\java\org\biojava\bio\structure\Chain.java:[28,-1] > cannot access org.biojava3.core.sequence.template.Sequence > [ERROR] bad class file: > C:\Users\radamek\.m2\repository\org\biojava\biojava3-core\3.0.6-SNAPSHOT\biojava3-core-3.0.6-SNAPSHOT.jar(org/biojava3/core/sequence/template/Sequence.class) > [ERROR] class file has wrong version 50.0, should be 49.0 > > Radomir wrote: >> >> Hello, i`m trying to apply my project with oracle and biojava. I`m trying >> to make a database for pairwise alignment ( FATCAT or CE ). These >> algorithms are in biojava3+ packages. When i`m loading jar`s to mine >> database i got error ( oracle is running on 1.5 jdk and biojava 3 is >> compiled on 1.6, there are no chances to upgrade jdk on oracle ).. I find >> on biojava wiki that version 3.0 of biojava is running on 1.5+ but when i >> loaded these version to my database there was the same error. Here is my >> question - is there any chances to get biojava 3 compiled with jdk 1.5 ? >> ? Sorry for my english >> > > -- View this message in context: http://old.nabble.com/BioJava%2C-oracle-problem-with-jdk-tp34984653p35040215.html Sent from the BioJava mailing list archive at Nabble.com. From radomir.adamek at hotmail.com Tue Feb 19 04:00:01 2013 From: radomir.adamek at hotmail.com (Radomir) Date: Tue, 19 Feb 2013 01:00:01 -0800 (PST) Subject: [Biojava-l] BioJava, oracle problem with jdk In-Reply-To: <34984653.post@talk.nabble.com> References: <34984653.post@talk.nabble.com> Message-ID: <35040216.post@talk.nabble.com> Hello, sorry for spam. I solved the last error but i got new one. I can compile core package to version 1.5 jdk but when i try to compile phylo package i got error like that: [INFO] biojava ........................................... SUCCESS [0.748s] [INFO] biojava3-core ..................................... SUCCESS [7.076s] [INFO] biojava3-phylo .................................... FAILURE [0.321s] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.5.1:compile (default-compile) on project biojava3-phylo: Compilation failure [ERROR] Failure executing javac, but could not parse the error: [ERROR] javac: invalid flag: -s [ERROR] Usage: javac can anyone help me?? i don`t have idea what i`m making wrong. Radomir wrote: > > Hello, i`m trying to apply my project with oracle and biojava. I`m trying > to make a database for pairwise alignment ( FATCAT or CE ). These > algorithms are in biojava3+ packages. When i`m loading jar`s to mine > database i got error ( oracle is running on 1.5 jdk and biojava 3 is > compiled on 1.6, there are no chances to upgrade jdk on oracle ).. I find > on biojava wiki that version 3.0 of biojava is running on 1.5+ but when i > loaded these version to my database there was the same error. Here is my > question - is there any chances to get biojava 3 compiled with jdk 1.5 ? ? > Sorry for my english > -- View this message in context: http://old.nabble.com/BioJava%2C-oracle-problem-with-jdk-tp34984653p35040216.html Sent from the BioJava mailing list archive at Nabble.com. From amr_alhossary at hotmail.com Tue Feb 19 04:21:50 2013 From: amr_alhossary at hotmail.com (Amr AL-HOSSARY) Date: Tue, 19 Feb 2013 17:21:50 +0800 Subject: [Biojava-l] BioJava, oracle problem with jdk In-Reply-To: <35040216.post@talk.nabble.com> References: <34984653.post@talk.nabble.com>,<35040216.post@talk.nabble.com> Message-ID: It's something in your eclipse/maven settings related to output folder.There is already a switch in javac (version 1.7) called -s -s Specify where to place generated source files I am not sure if it is present in version 5 or not.Any way, if you can, just remove it. Regards,Amr Best Regards, Amr AL-HOSSARY Amr Ali AL-HOSSARY | Ph.D. Student | International PhD program in Computational Biology and Bioinformatics | School of Computer Engineering | Nanyang Technological University | Singapore | Email: amra0001 at e.ntu.edu.sg | > Date: Tue, 19 Feb 2013 01:00:01 -0800 > From: radomir.adamek at hotmail.com > To: biojava-l at lists.open-bio.org > Subject: Re: [Biojava-l] BioJava, oracle problem with jdk > > > Hello, sorry for spam. I solved the last error but i got new one. I can > compile core package to version 1.5 jdk but when i try to compile phylo > package i got error like that: > [INFO] biojava ........................................... SUCCESS [0.748s] > [INFO] biojava3-core ..................................... SUCCESS [7.076s] > [INFO] biojava3-phylo .................................... FAILURE [0.321s] > > Failed to execute goal > org.apache.maven.plugins:maven-compiler-plugin:2.5.1:compile > (default-compile) on project biojava3-phylo: Compilation failure > [ERROR] Failure executing javac, but could not parse the error: > [ERROR] javac: invalid flag: -s > [ERROR] Usage: javac > > can anyone help me?? i don`t have idea what i`m making wrong. > > Radomir wrote: > > > > Hello, i`m trying to apply my project with oracle and biojava. I`m trying > > to make a database for pairwise alignment ( FATCAT or CE ). These > > algorithms are in biojava3+ packages. When i`m loading jar`s to mine > > database i got error ( oracle is running on 1.5 jdk and biojava 3 is > > compiled on 1.6, there are no chances to upgrade jdk on oracle ).. I find > > on biojava wiki that version 3.0 of biojava is running on 1.5+ but when i > > loaded these version to my database there was the same error. Here is my > > question - is there any chances to get biojava 3 compiled with jdk 1.5 ? ? > > Sorry for my english > > > > -- > View this message in context: http://old.nabble.com/BioJava%2C-oracle-problem-with-jdk-tp34984653p35040216.html > Sent from the BioJava mailing list archive at Nabble.com. > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From nickengland at gmail.com Tue Feb 19 04:53:14 2013 From: nickengland at gmail.com (Nick England) Date: Tue, 19 Feb 2013 09:53:14 +0000 Subject: [Biojava-l] Reading SCF files In-Reply-To: References: Message-ID: I get the same error message, it looks like a bug in BioJava parsing comments from SCF files. My SCF files load fine, but they don't have comments inside. Has anyone else seen this problem before? - Nick On 18 February 2013 19:48, Janier J. Ram?rez wrote: > Traying to read this SCF file, I get the following errors and warnings, > the fail is at: > > Chromatogram scf = ChromatogramFactory.create(stream); > > Warning: the code set (2) is not specifically supported. (It may still > work, though.) > Exception in thread "main" java.lang.IllegalArgumentException: Can't skip > backwards: (newOffset==0) < (offset==128) > at org.biojava.bio.program.scf.SCF$Parser.skipTo(SCF.java:424) > at > org.biojava.bio.program.scf.SCF$Parser.parseComments(SCF.java:384) > at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:372) > at > org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:206) > at org.biojava.bio.program.scf.SCF.load(SCF.java:149) > at org.biojava.bio.program.scf.SCF.create(SCF.java:133) > at > org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:117) > at javaapplication1.NewClass.main(NewClass.java:44) > > > And this is my code > > public class NewClass { > > public static void main(String[] args) > throws Exception { > JFileChooser fileChooser = new JFileChooser(); > fileChooser.setDialogTitle("Abrir"); > fileChooser.setMultiSelectionEnabled(true); > > int a = JFileChooser.APPROVE_OPTION; > > fileChooser.setFileFilter(new Filtro("scf", "")); > if (a == fileChooser.showOpenDialog(null)) { > > File file = fileChooser.getSelectedFile(); > InputStream stream = new FileInputStream(file); > > Chromatogram scf = ChromatogramFactory.create(stream); > /***Here is the fail***/ > > stream.close(); > Alignment data = scf.getBaseCalls(); > String seq = data.symbolListForLabel("dna").seqString(); > } > > } > } > > Thanks > > ----- Mensaje original ----- > De: "Nick England" > Para: "Janier J. Ram?rez" > CC: biojava-l at lists.open-bio.org > Enviados: Lunes, 18 de Febrero 2013 5:13:12 > Asunto: Re: [Biojava-l] Reading SCF files > > Janier, > > Here is a snippet which should read in SCF files for you, you will have to > have BioJava 1.0 for this to work. > > File file = new File(String "your path here"); > InputStream stream = new FileInputStream(file); > Chromatogram scf= ChromatogramFactory.create(stream); > stream.close(); > Alignment data = scf.getBaseCalls(); > String seq=data.symbolListForLabel("dna").seqString(); > > Cheers, > > Nick > > > > On 18 February 2013 05:09, Janier J. Ram?rez < > jjramirez at estudiantes.uci.cu > wrote: > > > Yes that's ok, Now I need an example of how given the path of the scf > file, get the secuence, to them parse it to fasta, or if I can do it > directly from scf to fasta. > > Thanks for your time > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > > From radomir.adamek at hotmail.com Tue Feb 19 05:08:44 2013 From: radomir.adamek at hotmail.com (Radomir) Date: Tue, 19 Feb 2013 02:08:44 -0800 (PST) Subject: [Biojava-l] BioJava, oracle problem with jdk In-Reply-To: <34984653.post@talk.nabble.com> References: <34984653.post@talk.nabble.com> Message-ID: <35040465.post@talk.nabble.com> Ahh, i`m almost home. Now i have problem with 2 methods from java 1.6. In alignment package there is a 2 methods copyof() and isempty() that can`t be compile with 1.5: [ERROR] C:\Users\radamek\workspace\maven.1361187141685\biojava\biojava3-alignment\src\main\java\org\biojava3\alignment\SimpleSubstitutionMatrix.java:[145,33] cannot find symbol [ERROR] symbol : method isEmpty() [ERROR] location: class java.lang.String [ERROR] C:\Users\radamek\workspace\maven.1361187141685\biojava\biojava3-alignment\src\main\java\org\biojava3\alignment\SimpleSubstitutionMatrix.java:[185,28] cannot find symbol [ERROR] symbol : method copyOf(short[],int) [ERROR] location: class java.util.Arrays Can somebody help me?? i found that i should make new methods, i really don`t know how to do that ( i don`t know java very well..) Radomir wrote: > > Hello, i`m trying to apply my project with oracle and biojava. I`m trying > to make a database for pairwise alignment ( FATCAT or CE ). These > algorithms are in biojava3+ packages. When i`m loading jar`s to mine > database i got error ( oracle is running on 1.5 jdk and biojava 3 is > compiled on 1.6, there are no chances to upgrade jdk on oracle ).. I find > on biojava wiki that version 3.0 of biojava is running on 1.5+ but when i > loaded these version to my database there was the same error. Here is my > question - is there any chances to get biojava 3 compiled with jdk 1.5 ? ? > Sorry for my english > -- View this message in context: http://old.nabble.com/BioJava%2C-oracle-problem-with-jdk-tp34984653p35040465.html Sent from the BioJava mailing list archive at Nabble.com. From jjramirez at estudiantes.uci.cu Thu Feb 21 09:11:08 2013 From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=) Date: Thu, 21 Feb 2013 09:11:08 -0500 (EST) Subject: [Biojava-l] Bug Reading SCF files In-Reply-To: Message-ID: <6c83019b-3b8b-4942-9fb5-ec28e21ba57f@ucimail4.uci.cu> Hi comunity ! I need help reading SCF files, I have some SCF files that Biojava is unable to read, but in others tools these files open correctly. I just need to read the file and get the sequence. help please... Thanks Janier From andreas at sdsc.edu Thu Feb 21 11:05:41 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 21 Feb 2013 08:05:41 -0800 Subject: [Biojava-l] Bug Reading SCF files In-Reply-To: <6c83019b-3b8b-4942-9fb5-ec28e21ba57f@ucimail4.uci.cu> References: <6c83019b-3b8b-4942-9fb5-ec28e21ba57f@ucimail4.uci.cu> Message-ID: Hi Janier, did you try to remove the comment lines from your file? In an earlier thread that was suggested as a possible source of problems. I think we should add porting the Chromatogram parser to BioJava 3 to our open projects page... Andreas On Thu, Feb 21, 2013 at 6:11 AM, Janier J. Ram?rez < jjramirez at estudiantes.uci.cu> wrote: > Hi comunity ! > I need help reading SCF files, I have some SCF files that Biojava is > unable to read, but in others tools these files open correctly. > I just need to read the file and get the sequence. > > help please... > Thanks > > Janier > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- ----------------------------------------------------------------------- Dr. Andreas Prlic Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego (+1) 858.246.0526 ----------------------------------------------------------------------- From andreas at sdsc.edu Thu Feb 21 11:08:33 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 21 Feb 2013 08:08:33 -0800 Subject: [Biojava-l] GSOC 2013 projects Message-ID: Hi, a few people have contacted me off-list with possible ideas regarding google summer of code projects. I think it is important to move that discussion into the public. I'd suggest that people add a few lines with their ideas to the GSOC 2013 page on our wiki: http://biojava.org/wiki/Google_Summer_of_Code_2013 Andreas From andreas at sdsc.edu Thu Feb 21 11:47:35 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 21 Feb 2013 08:47:35 -0800 Subject: [Biojava-l] Bug Reading SCF files In-Reply-To: <8573827260165005279@unknownmsgid> References: <6c83019b-3b8b-4942-9fb5-ec28e21ba57f@ucimail4.uci.cu> <8573827260165005279@unknownmsgid> Message-ID: that would be great! Andreas On Thu, Feb 21, 2013 at 8:27 AM, Hannes Brandst?tter-M?ller < admin at hannes.oib.com> wrote: > I wanted to do that last year, I think. I'll take a look at it if I > can make some time after the move to github > > Sent from my mobile. Please excuse the brevity, spelling and punctuation. > > Am 21.02.2013 um 17:15 schrieb Andreas Prlic : > > > Hi Janier, > > > > did you try to remove the comment lines from your file? In an earlier > > thread that was suggested as a possible source of problems. > > > > I think we should add porting the Chromatogram parser to BioJava 3 to our > > open projects page... > > > > Andreas > > > > > > On Thu, Feb 21, 2013 at 6:11 AM, Janier J. Ram?rez < > > jjramirez at estudiantes.uci.cu> wrote: > > > >> Hi comunity ! > >> I need help reading SCF files, I have some SCF files that Biojava is > >> unable to read, but in others tools these files open correctly. > >> I just need to read the file and get the sequence. > >> > >> help please... > >> Thanks > >> > >> Janier > >> > >> _______________________________________________ > >> Biojava-l mailing list - Biojava-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > -- > > ----------------------------------------------------------------------- > > Dr. Andreas Prlic > > Senior Scientist, RCSB PDB Protein Data Bank > > University of California, San Diego > > (+1) 858.246.0526 > > ----------------------------------------------------------------------- > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > From jjramirez at estudiantes.uci.cu Thu Feb 21 14:41:14 2013 From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=) Date: Thu, 21 Feb 2013 14:41:14 -0500 (EST) Subject: [Biojava-l] Reading SCF Files In-Reply-To: <4d83136d-33ce-4922-be52-223c9e2e9e02@ucimail4.uci.cu> Message-ID: <6fafee59-8cca-4792-9e53-a977fea3e7af@ucimail4.uci.cu> Yes, I opened the file in notepad, but there are many rare characters, I don't know where are the comments, I did send you the files that I need to read. Janier -- From jeremy at lewi.us Tue Feb 26 11:14:27 2013 From: jeremy at lewi.us (Jeremy Lewi) Date: Tue, 26 Feb 2013 08:14:27 -0800 Subject: [Biojava-l] biojava, clouds, and contrail Message-ID: Hi BioJava users, I discovered BioJava the other day while looking for some java libraries to process reads. I've been working on an assembler, Contrail, http://sourceforge.net/apps/mediawiki/contrail-bio/index.php?title=Contrail, which uses map reduce. I'd like to get more involved in the bioinformatics community so I thought I'd say hello to this group. Unfortunately, when we first started coding Contrail I didn't do a proper Google search to see if their were existing libraries for things like DNA sequence manipulation we just rolled out own because it was faster. Anyways if folks want to chat more please let me know, Best J From chapmanb at 50mail.com Thu Feb 28 21:39:11 2013 From: chapmanb at 50mail.com (Brad Chapman) Date: Thu, 28 Feb 2013 21:39:11 -0500 Subject: [Biojava-l] 2013 BOSC/Broad Interoperability Hackathon + BOSC Codefest In-Reply-To: References: Message-ID: <87mwunsv1s.fsf@fastmail.fm> Michael; Thanks for publicizing these. I sent around a more general reminder about the events but definitely welcome Java folks to come out to the coding sessions (and BOSC itself). The hackathon at Broad will have a lot of programmers from the GenomeSpace team (http://www.genomespace.org/) so there will be plenty of Java object talk to go around, Brad > Just wanted to announce to and/or remind folks of two upcoming BOSC > and Biojava-related events: > > April 7-8, 2013: BOSC/Broad Interoperability Hackathon, Cambridge, MA > http://www.broadinstitute.org/events/interoperability-hackathon-2013/home > > July 17-18, 2013: Codefest 2013, Berlin > http://www.open-bio.org/wiki/Codefest_2013 > > michael > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From radomir.adamek at hotmail.com Wed Feb 6 07:03:30 2013 From: radomir.adamek at hotmail.com (Radomir) Date: Tue, 5 Feb 2013 23:03:30 -0800 (PST) Subject: [Biojava-l] BioJava, oracle problem with jdk Message-ID: <34984653.post@talk.nabble.com> Hello, i`m trying to apply my project with oracle and biojava. I`m trying to make a database for pairwise alignment ( FATCAT or CE ). These algorithms are in biojava3+ packages. When i`m loading jar`s to mine database i got error ( oracle is running on 1.5 jdk and biojava 3 is compiled on 1.6, there are no chances to upgrade jdk on oracle ).. I find on biojava wiki that version 3.0 of biojava is running on 1.5+ but when i loaded these version to my database there was the same error. Here is my question - is there any chances to get biojava 3 compiled with jdk 1.5 ? ? Sorry for my english -- View this message in context: http://old.nabble.com/BioJava%2C-oracle-problem-with-jdk-tp34984653p34984653.html Sent from the BioJava mailing list archive at Nabble.com. From amr_alhossary at hotmail.com Wed Feb 6 07:13:55 2013 From: amr_alhossary at hotmail.com (Amr AL-HOSSARY) Date: Wed, 6 Feb 2013 15:13:55 +0800 Subject: [Biojava-l] BioJava, oracle problem with jdk In-Reply-To: <34984653.post@talk.nabble.com> References: <34984653.post@talk.nabble.com> Message-ID: Greetings Radomir, If you are using Eclipse, you can obtain a checkout copy of the source code, compile it on Java 6, and in the compiler settings, search for an option to generate Java 5 compatible byte code, generate jars, and use them. You may need to compile them yourself (not as Maven projects), but I am not sure of that. Best Regards, Amr AL-HOSSARY Amr Ali AL-HOSSARY | Ph.D. Student | International PhD program in Computational Biology and Bioinformatics | School of Computer Engineering | Nanyang Technological University | Singapore | Email: amra0001 at e.ntu.edu.sg | > Date: Tue, 5 Feb 2013 23:03:30 -0800 > From: radomir.adamek at hotmail.com > To: biojava-l at lists.open-bio.org > Subject: [Biojava-l] BioJava, oracle problem with jdk > > > Hello, i`m trying to apply my project with oracle and biojava. I`m trying to > make a database for pairwise alignment ( FATCAT or CE ). These algorithms > are in biojava3+ packages. When i`m loading jar`s to mine database i got > error ( oracle is running on 1.5 jdk and biojava 3 is compiled on 1.6, there > are no chances to upgrade jdk on oracle ).. I find on biojava wiki that > version 3.0 of biojava is running on 1.5+ but when i loaded these version to > my database there was the same error. Here is my question - is there any > chances to get biojava 3 compiled with jdk 1.5 ? ? Sorry for my english > -- > View this message in context: http://old.nabble.com/BioJava%2C-oracle-problem-with-jdk-tp34984653p34984653.html > Sent from the BioJava mailing list archive at Nabble.com. > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From darnells at dnastar.com Wed Feb 6 16:24:55 2013 From: darnells at dnastar.com (Steve Darnell) Date: Wed, 6 Feb 2013 16:24:55 +0000 Subject: [Biojava-l] BioJava, oracle problem with jdk In-Reply-To: <34984653.post@talk.nabble.com> References: <34984653.post@talk.nabble.com> Message-ID: Hi Radomir, I expect you must be using a Mac with a PPC or 32-bit Intel CPU. Apple Java 6 is not available for PPC architecture nor 32-bit Intel machines running OS X 10.5 or lower. Java 6 is available on Windows XP/Vista/7, Linux, and Mac OS X 10.5 (64-bit only)/10.6+. If you must use Java 5, your options are: * Build BioJava yourself (as Amr suggested): http://biojava.org/wiki/Get_source, http://biojava.org/wiki/BioJava3_eclipse * Try SoyLatte: http://landonf.bikemonkey.org/static/soylatte/, Java 6 port for Mac OS X 10.4, 10.5 (Intel) If you go the SoyLatte route, be prepared to pray for it to work. It is several years old. If it were me, I'd update my Mac to 10.6 then hope the mainboard doesn't fail. I'm not a huge fan of 10.7+, but I'll be forced to go there eventually. ~Steve -----Original Message----- From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Radomir Sent: Wednesday, February 06, 2013 1:04 AM To: biojava-l at lists.open-bio.org Subject: [Biojava-l] BioJava, oracle problem with jdk Hello, i`m trying to apply my project with oracle and biojava. I`m trying to make a database for pairwise alignment ( FATCAT or CE ). These algorithms are in biojava3+ packages. When i`m loading jar`s to mine database i got error ( oracle is running on 1.5 jdk and biojava 3 is compiled on 1.6, there are no chances to upgrade jdk on oracle ).. I find on biojava wiki that version 3.0 of biojava is running on 1.5+ but when i loaded these version to my database there was the same error. Here is my question - is there any chances to get biojava 3 compiled with jdk 1.5 ? ? Sorry for my english -- View this message in context: http://old.nabble.com/BioJava%2C-oracle-problem-with-jdk-tp34984653p34984653.html Sent from the BioJava mailing list archive at Nabble.com. _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From andreas at sdsc.edu Wed Feb 6 16:54:37 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Wed, 6 Feb 2013 08:54:37 -0800 Subject: [Biojava-l] preparations for Google Summer of Code Message-ID: Hi, Google has not released yet if they will sponsor another Google Summer of Code this year, but we should still try to prepare, so we are ready if/when the announcement comes out. Any project ideas that we want people to work on this summer? I stated a new wiki page for this at http://biojava.org/wiki/Google_Summer_of_Code_2013 Andreas From pwrose at ucsd.edu Mon Feb 11 18:12:56 2013 From: pwrose at ucsd.edu (Peter Rose) Date: Mon, 11 Feb 2013 18:12:56 +0000 Subject: [Biojava-l] [Job] Take the RCSB PDB site to the next level Message-ID: The RCSB PDB at the University of California, San Diego is looking for a talented Java Developer/Lead Web Architect: The RCSB Protein Data Bank (http://www.rcsb.org) is one of the premier biological databases worldwide with a growing user base of currently about 300,000 unique users per month. We constantly strive to make our site perform better, make it look nicer and offer new and exciting scientific applications to our diverse user base that includes scientists, students, teachers and other researchers. We offer a flexible work environment in a dynamic team. We offer the challenge to take the RCSB PDB web site to the next level. For this we are looking for a lead architect and Java web developer. You will provide expertise and leadership in enhancing the data warehouse and middle layer of the PDB website's 3-tier architecture by working with a team of scientists and software developers. Translate new and emergent requirements for the website into strategic plans to select the best web technologies and architectures for the PDB site. Author functional requirements, technical design documents, and project plans. Incorporate advanced scientific query and analysis tools, and novel representation of results in the web application. Provide technical leadership, guidance, and training on new web technologies to RCSB team and provide high level and implementation level suggestions for improving design, coding, and testing methodologies. Develop best project management and software engineering practices. Our technology stack includes Java, MySQL, Hibernate, and Memcached. UC San Diego is an Equal Opportunity / Staff Affirmative Action Employer that values a diverse workforce and provides reasonable accommodations to people with disabilities. We offer a generous benefits package: http://www.sdsc.edu/about/Careers.html. Please apply online at: http://jobs.ucsd.edu/bulletin/job.aspx?cat=information&sortby=post&jobnum_in=64091 QUALIFICATIONS * BS Degree in Computer Science or comparable combination of education and experience with considerable focus in Java software development. * Established demonstrated work experience in the role of an architect and developer on medium to large size database-driven web applications using Java technology and standards. * Advanced experience with database design, Structured Query Language and RDBMS's such as MySQL, and object-relational mappings. Expertise in web application server (i.e., Tomcat) administration, configuration, trouble shooting, and performance tuning. * Established expertise in software life cycle methodologies. Experience with build tools such as Maven and Ant, and continuous integration systems such as Cruise Control. Experience with project tracking tools such as Jira . ________________________________________________ Peter Rose, Ph.D. Scientific Lead RCSB Protein Data Bank (http://www.rcsb.org) San Diego Supercomputer Center (SDSC) and Skaggs School of Pharmacy and Pharmaceutical Sciences Pharmaceutical Sciences Building University of California San Diego 9500 Gilman Drive, Mailcode 0743 La Jolla, CA 92093-0743 Email: pwrose at ucsd.edu Voice: (858) 822-5497 Fax: (858) 822-0873 From andreas at sdsc.edu Mon Feb 11 19:18:52 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 11 Feb 2013 11:18:52 -0800 Subject: [Biojava-l] Fwd: [GSoC Mentors Announce] Google Summer of Code 2013 In-Reply-To: References: Message-ID: Hi, Google summer of code 2013 has been announced... Anybody interested in mentoring, or suggesting projects for this year? Andreas ---------- Forwarded message ---------- From: Carol Smith Date: Mon, Feb 11, 2013 at 11:02 AM Subject: [GSoC Mentors Announce] Google Summer of Code 2013 To: gsoc-mentors-announce at googlegroups.com Hi GSoC mentors and org admins, We've announced that we're doing Google Summer of Code 2013 [1]. Yay! If you would like to help spread the word about GSoC, we have presentations [2], logos [3], and flyers [4] for you to use. Please host meetups, tell your friends and colleagues about the program, go to conferences, talk to people about the program, and just generally do all the awesome word-of-mouth stuff you do every year to promote the program. The GSoC calendar, FAQ, and events timeline have all been updated with this year's important dates, so please refer to those for the milestones for this year's program. NB: the normal timeline for the program has been modified for this year. You'll probably want to examine the dates closely to make sure you know when important things are happening. Please consider translating the presentations and/or flyers into your native language and submitting them directly to me to post on the wiki. Localization for our material is integral to reaching the widest possible audience around the world. If you decide to translate a flyer, please fill out our form to request a thank you gift for your effort. [5] If you decide to host a meetup, please email me to let me know the date, time, and location so I can put it on the GSoC calendar. Also, remember to take pictures at your meetup and write up a blog post for our blog using our provided template for formatting [6]. If you need promotional items for your attendees, please fill out our form [7] to request some; we're happy to send some along. We can provide up to about 25 pens, notebooks, or stickers and/or a few t-shirts. Please keep in mind, though, that shipping restrictions and timeline vary country-to-country; request items early to make sure they get there on time! If you have questions about hosting meetups, please see the section in our FAQ [8]. Please also consider applying to participate as an organization again this year or maybe joining as a mentor for your favorite organization if they are selected this year. We rely on you for your help for the success of this program, so thank you in advance for all the work you do! [1] - http://google-opensource.blogspot.com/2013/02/flip-bits-not-burgers-google-summer-of.html [2] - http://code.google.com/p/google-summer-of-code/wiki/ProgramPresentations [3] - http://code.google.com/p/google-summer-of-code/wiki/GsocLogos [4] - http://code.google.com/p/google-summer-of-code/wiki/GsocFlyers [5] - http://goo.gl/gEHDO [6] - http://goo.gl/wbZrt [7] - http://goo.gl/0BsR8 [8] - http://goo.gl/2NGfp Cheers, Carol -- You received this message because you are subscribed to the Google Groups "Google Summer of Code Mentors Announce List" group. To unsubscribe from this group and stop receiving emails from it, send an email to gsoc-mentors-announce+unsubscribe at googlegroups.com. Visit this group at http://groups.google.com/group/gsoc-mentors-announce?hl=en-US. For more options, visit https://groups.google.com/groups/opt_out. From heuermh at gmail.com Mon Feb 11 21:33:59 2013 From: heuermh at gmail.com (Michael Heuer) Date: Mon, 11 Feb 2013 15:33:59 -0600 Subject: [Biojava-l] 2013 BOSC/Broad Interoperability Hackathon + BOSC Codefest Message-ID: All, Just wanted to announce to and/or remind folks of two upcoming BOSC and Biojava-related events: April 7-8, 2013: BOSC/Broad Interoperability Hackathon, Cambridge, MA http://www.broadinstitute.org/events/interoperability-hackathon-2013/home July 17-18, 2013: Codefest 2013, Berlin http://www.open-bio.org/wiki/Codefest_2013 michael From saidi34 at hushmail.com Tue Feb 12 17:39:07 2013 From: saidi34 at hushmail.com (saidi34 at hushmail.com) Date: Tue, 12 Feb 2013 12:39:07 -0500 Subject: [Biojava-l] =?utf-8?q?A_Ph=2ED=2E_Student=E2=80=99s_CRY_for_Help?= Message-ID: <20130212173907.6C263E6726@smtp.hushmail.com> A Ph.D. Student?s CRY for Help To: Prof. Hamid Arabnia, WORLDCOMP Coordinator, Professor of Computer Science, University of Georgia, USA Prof. Hamid Arabnia, I am a student from Africa and I am in the final stages of my Ph.D. work. I have a journal paper in ACM and a conference paper in WORLDCOMP. As per my university policy, I am required to have at least two research papers in peer-reviewed (refereed) international conferences or journals before I submit my synopsis/dissertation. While everything was fine, recently, WORLDCOMP was declared as a bogus conference with evidences and endorsements from scientists: https://sites.google.com/site/worlddump1 Also see http://worldcomp-fake-bogus.blogspot.com Now, my university officials have stopped me from submitting the dissertation stating that WORLDCOMP is not peer-reviewed due to the evidences in these websites. They said that WORLDCOMP is completely fake and that?s why you have not responded to the open challenge at https://sites.google.com/site/dumpconf or https://sites.google.com/site/moneycomp1 I sent many emails to you requesting to respond to the open challenge and prove that WORLDCOMP is not fake so that I can show your response to my university officials and convince them and submit my dissertation. I also asked you to email me the reviews for my paper (I never received them, although your acceptance email stated that the paper was reviewed by two experts) but you are not responding. Recall that when I met you in WORLDCOMP, you offered me a reference letter and invited me to organize a session in the next conference and promised free registration for my next paper if I get at least five registered papers fr om others. Now I am shocked with your silence. I am clueless on what to do as I will forfeit my student status unless I submit the dissertation soon. I am facing humiliation here. I was attracted by the keynote speakers, sponsors, tutorials, and University of Georgia name at WORLDCOMP website. Now I feel that I made a very critical mistake by submitting to WORLDCOMP. As the last resort, I am posting to this mailing list/forum (where WORLDCOMP details were published in the past I think) so that you understand the seriousness. I once again ask you to provide a detailed response at WORLDCOMP?s website and prove that it is not a fake (and also email me my paper reviews). I request you to focus on this issue than organizing the next conference (and create more victims like me). I hope you still have moral values. My elderly parents are dependent on me and I am crying for help. I openly beg your response! Respectfully, Saidi (this is my nickname and I am using it to avoid further humiliation. I know that you will easily identify me from this nickname and from my background mentioned above). To the forum/list owner: please understand my situation and publish this message and it will help other researchers to be more careful while choosing a conference. To the members: please help me getting a response from Prof. Arabnia. From andreas at sdsc.edu Thu Feb 14 00:10:29 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Wed, 13 Feb 2013 16:10:29 -0800 Subject: [Biojava-l] BioJava SVN moving to github Message-ID: Hi, as we have discussed several times over the last months, the time has come to migrate the BioJava SVN repository to github. I want to thank Spencer Bliven who has volunteered to be in charge of this migration and who will guide us through this process. Thanks, Spencer! Andreas From hlapp at drycafe.net Thu Feb 14 04:21:54 2013 From: hlapp at drycafe.net (Hilmar Lapp) Date: Wed, 13 Feb 2013 23:21:54 -0500 Subject: [Biojava-l] BioJava SVN moving to github In-Reply-To: References: Message-ID: On Feb 13, 2013, at 7:10 PM, Andreas Prlic wrote: > as we have discussed several times over the last months, the time has come > to migrate the BioJava SVN repository to github. Great! -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From jprocter at compbio.dundee.ac.uk Fri Feb 15 14:50:35 2013 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Fri, 15 Feb 2013 14:50:35 +0000 Subject: [Biojava-l] BioJava SVN moving to github In-Reply-To: References: Message-ID: <511E4B3B.1050909@compbio.dundee.ac.uk> On Thu Feb 14 04:21:54 2013, Hilmar Lapp wrote: > > On Feb 13, 2013, at 7:10 PM, Andreas Prlic wrote: > >> as we have discussed several times over the last months, the time has come >> to migrate the BioJava SVN repository to github. May the g-force be with you, Spencer! ..Jim. From jjramirez at estudiantes.uci.cu Mon Feb 18 03:24:44 2013 From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=) Date: Sun, 17 Feb 2013 22:24:44 -0500 (EST) Subject: [Biojava-l] Reading SCF files In-Reply-To: Message-ID: <9b0b495e-a4c6-4e0c-923d-791ae836ae51@ucimail4.uci.cu> Hello, I need to read an SCF file using BioJava to finally show the chromatogram, but I don't know what version of BioJava to use Thanks for your time -- There is no knowledge, that is not power From andreas at sdsc.edu Mon Feb 18 04:25:32 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Sun, 17 Feb 2013 20:25:32 -0800 Subject: [Biojava-l] Reading SCF files In-Reply-To: <9b0b495e-a4c6-4e0c-923d-791ae836ae51@ucimail4.uci.cu> References: <9b0b495e-a4c6-4e0c-923d-791ae836ae51@ucimail4.uci.cu> Message-ID: Hi Janier, that is part of BioJava 1... Andreas On Sun, Feb 17, 2013 at 7:24 PM, Janier J. Ram?rez < jjramirez at estudiantes.uci.cu> wrote: > Hello, I need to read an SCF file using BioJava to finally show the > chromatogram, but I don't know what version of BioJava to use > > Thanks for your time > -- > There is no knowledge, that is not power > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From jjramirez at estudiantes.uci.cu Mon Feb 18 05:09:08 2013 From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=) Date: Mon, 18 Feb 2013 00:09:08 -0500 (EST) Subject: [Biojava-l] Reading SCF files In-Reply-To: <9b0b495e-a4c6-4e0c-923d-791ae836ae51@ucimail4.uci.cu> Message-ID: Yes that's ok, Now I need an example of how given the path of the scf file, get the secuence, to them parse it to fasta, or if I can do it directly from scf to fasta. Thanks for your time From nickengland at gmail.com Mon Feb 18 10:13:12 2013 From: nickengland at gmail.com (Nick England) Date: Mon, 18 Feb 2013 10:13:12 +0000 Subject: [Biojava-l] Reading SCF files In-Reply-To: References: <9b0b495e-a4c6-4e0c-923d-791ae836ae51@ucimail4.uci.cu> Message-ID: Janier, Here is a snippet which should read in SCF files for you, you will have to have BioJava 1.0 for this to work. File file = new File(String "your path here"); InputStream stream = new FileInputStream(file); Chromatogram scf= ChromatogramFactory.create(stream); stream.close(); Alignment data = scf.getBaseCalls(); String seq=data.symbolListForLabel("dna").seqString(); Cheers, Nick On 18 February 2013 05:09, Janier J. Ram?rez wrote: > Yes that's ok, Now I need an example of how given the path of the scf > file, get the secuence, to them parse it to fasta, or if I can do it > directly from scf to fasta. > > Thanks for your time > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From radomir.adamek at hotmail.com Mon Feb 18 11:46:03 2013 From: radomir.adamek at hotmail.com (Radomir) Date: Mon, 18 Feb 2013 03:46:03 -0800 (PST) Subject: [Biojava-l] BioJava, oracle problem with jdk In-Reply-To: <34984653.post@talk.nabble.com> References: <34984653.post@talk.nabble.com> Message-ID: <35036008.post@talk.nabble.com> Hi, thanks for reply. I`m having more problems with "recompiling" from 1.6 to 1.5. I have done everything like u told me. When i`m trying to clean install with maven compiler i got error with version. Can somebody tell me its possible to compile biojava 3 with 1.5 jdk? I don`t have idea how to do that and its very important for me ( my final project on my studies ). Here is a part of error from compiler: [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.5.1:compile (default-compile) on project biojava3-structure: Compilation failure [ERROR] C:\Users\radamek\workspace\maven.1361187141685\biojava\biojava3-structure\src\main\java\org\biojava\bio\structure\Chain.java:[28,-1] cannot access org.biojava3.core.sequence.template.Sequence [ERROR] bad class file: C:\Users\radamek\.m2\repository\org\biojava\biojava3-core\3.0.6-SNAPSHOT\biojava3-core-3.0.6-SNAPSHOT.jar(org/biojava3/core/sequence/template/Sequence.class) [ERROR] class file has wrong version 50.0, should be 49.0 Radomir wrote: > > Hello, i`m trying to apply my project with oracle and biojava. I`m trying > to make a database for pairwise alignment ( FATCAT or CE ). These > algorithms are in biojava3+ packages. When i`m loading jar`s to mine > database i got error ( oracle is running on 1.5 jdk and biojava 3 is > compiled on 1.6, there are no chances to upgrade jdk on oracle ).. I find > on biojava wiki that version 3.0 of biojava is running on 1.5+ but when i > loaded these version to my database there was the same error. Here is my > question - is there any chances to get biojava 3 compiled with jdk 1.5 ? ? > Sorry for my english > -- View this message in context: http://old.nabble.com/BioJava%2C-oracle-problem-with-jdk-tp34984653p35036008.html Sent from the BioJava mailing list archive at Nabble.com. From radomir.adamek at hotmail.com Tue Feb 19 08:59:19 2013 From: radomir.adamek at hotmail.com (Radomir) Date: Tue, 19 Feb 2013 00:59:19 -0800 (PST) Subject: [Biojava-l] BioJava, oracle problem with jdk In-Reply-To: <35036008.post@talk.nabble.com> References: <34984653.post@talk.nabble.com> <35036008.post@talk.nabble.com> Message-ID: <35040215.post@talk.nabble.com> Hello, sorry for spam. I solved the last error but i got new one. I can compile core package to version 1.5 jdk but when i try to compile phylo package i got error like that: [INFO] biojava ........................................... SUCCESS [0.748s] [INFO] biojava3-core ..................................... SUCCESS [7.076s] [INFO] biojava3-phylo .................................... FAILURE [0.321s] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.5.1:compile (default-compile) on project biojava3-phylo: Compilation failure [ERROR] Failure executing javac, but could not parse the error: [ERROR] javac: invalid flag: -s [ERROR] Usage: javac can anyone help me?? i don`t have idea what i`m making wrong. Radomir wrote: > > Hi, thanks for reply. I`m having more problems with "recompiling" from 1.6 > to 1.5. I have done everything like u told me. When i`m trying to clean > install with maven compiler i got error with version. Can somebody tell me > its possible to compile biojava 3 with 1.5 jdk? I don`t have idea how to > do that and its very important for me ( my final project on my studies ). > Here is a part of error from compiler: > > [ERROR] Failed to execute goal > org.apache.maven.plugins:maven-compiler-plugin:2.5.1:compile > (default-compile) on project biojava3-structure: Compilation failure > [ERROR] > C:\Users\radamek\workspace\maven.1361187141685\biojava\biojava3-structure\src\main\java\org\biojava\bio\structure\Chain.java:[28,-1] > cannot access org.biojava3.core.sequence.template.Sequence > [ERROR] bad class file: > C:\Users\radamek\.m2\repository\org\biojava\biojava3-core\3.0.6-SNAPSHOT\biojava3-core-3.0.6-SNAPSHOT.jar(org/biojava3/core/sequence/template/Sequence.class) > [ERROR] class file has wrong version 50.0, should be 49.0 > > Radomir wrote: >> >> Hello, i`m trying to apply my project with oracle and biojava. I`m trying >> to make a database for pairwise alignment ( FATCAT or CE ). These >> algorithms are in biojava3+ packages. When i`m loading jar`s to mine >> database i got error ( oracle is running on 1.5 jdk and biojava 3 is >> compiled on 1.6, there are no chances to upgrade jdk on oracle ).. I find >> on biojava wiki that version 3.0 of biojava is running on 1.5+ but when i >> loaded these version to my database there was the same error. Here is my >> question - is there any chances to get biojava 3 compiled with jdk 1.5 ? >> ? Sorry for my english >> > > -- View this message in context: http://old.nabble.com/BioJava%2C-oracle-problem-with-jdk-tp34984653p35040215.html Sent from the BioJava mailing list archive at Nabble.com. From radomir.adamek at hotmail.com Tue Feb 19 09:00:01 2013 From: radomir.adamek at hotmail.com (Radomir) Date: Tue, 19 Feb 2013 01:00:01 -0800 (PST) Subject: [Biojava-l] BioJava, oracle problem with jdk In-Reply-To: <34984653.post@talk.nabble.com> References: <34984653.post@talk.nabble.com> Message-ID: <35040216.post@talk.nabble.com> Hello, sorry for spam. I solved the last error but i got new one. I can compile core package to version 1.5 jdk but when i try to compile phylo package i got error like that: [INFO] biojava ........................................... SUCCESS [0.748s] [INFO] biojava3-core ..................................... SUCCESS [7.076s] [INFO] biojava3-phylo .................................... FAILURE [0.321s] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.5.1:compile (default-compile) on project biojava3-phylo: Compilation failure [ERROR] Failure executing javac, but could not parse the error: [ERROR] javac: invalid flag: -s [ERROR] Usage: javac can anyone help me?? i don`t have idea what i`m making wrong. Radomir wrote: > > Hello, i`m trying to apply my project with oracle and biojava. I`m trying > to make a database for pairwise alignment ( FATCAT or CE ). These > algorithms are in biojava3+ packages. When i`m loading jar`s to mine > database i got error ( oracle is running on 1.5 jdk and biojava 3 is > compiled on 1.6, there are no chances to upgrade jdk on oracle ).. I find > on biojava wiki that version 3.0 of biojava is running on 1.5+ but when i > loaded these version to my database there was the same error. Here is my > question - is there any chances to get biojava 3 compiled with jdk 1.5 ? ? > Sorry for my english > -- View this message in context: http://old.nabble.com/BioJava%2C-oracle-problem-with-jdk-tp34984653p35040216.html Sent from the BioJava mailing list archive at Nabble.com. From amr_alhossary at hotmail.com Tue Feb 19 09:21:50 2013 From: amr_alhossary at hotmail.com (Amr AL-HOSSARY) Date: Tue, 19 Feb 2013 17:21:50 +0800 Subject: [Biojava-l] BioJava, oracle problem with jdk In-Reply-To: <35040216.post@talk.nabble.com> References: <34984653.post@talk.nabble.com>,<35040216.post@talk.nabble.com> Message-ID: It's something in your eclipse/maven settings related to output folder.There is already a switch in javac (version 1.7) called -s -s Specify where to place generated source files I am not sure if it is present in version 5 or not.Any way, if you can, just remove it. Regards,Amr Best Regards, Amr AL-HOSSARY Amr Ali AL-HOSSARY | Ph.D. Student | International PhD program in Computational Biology and Bioinformatics | School of Computer Engineering | Nanyang Technological University | Singapore | Email: amra0001 at e.ntu.edu.sg | > Date: Tue, 19 Feb 2013 01:00:01 -0800 > From: radomir.adamek at hotmail.com > To: biojava-l at lists.open-bio.org > Subject: Re: [Biojava-l] BioJava, oracle problem with jdk > > > Hello, sorry for spam. I solved the last error but i got new one. I can > compile core package to version 1.5 jdk but when i try to compile phylo > package i got error like that: > [INFO] biojava ........................................... SUCCESS [0.748s] > [INFO] biojava3-core ..................................... SUCCESS [7.076s] > [INFO] biojava3-phylo .................................... FAILURE [0.321s] > > Failed to execute goal > org.apache.maven.plugins:maven-compiler-plugin:2.5.1:compile > (default-compile) on project biojava3-phylo: Compilation failure > [ERROR] Failure executing javac, but could not parse the error: > [ERROR] javac: invalid flag: -s > [ERROR] Usage: javac > > can anyone help me?? i don`t have idea what i`m making wrong. > > Radomir wrote: > > > > Hello, i`m trying to apply my project with oracle and biojava. I`m trying > > to make a database for pairwise alignment ( FATCAT or CE ). These > > algorithms are in biojava3+ packages. When i`m loading jar`s to mine > > database i got error ( oracle is running on 1.5 jdk and biojava 3 is > > compiled on 1.6, there are no chances to upgrade jdk on oracle ).. I find > > on biojava wiki that version 3.0 of biojava is running on 1.5+ but when i > > loaded these version to my database there was the same error. Here is my > > question - is there any chances to get biojava 3 compiled with jdk 1.5 ? ? > > Sorry for my english > > > > -- > View this message in context: http://old.nabble.com/BioJava%2C-oracle-problem-with-jdk-tp34984653p35040216.html > Sent from the BioJava mailing list archive at Nabble.com. > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From nickengland at gmail.com Tue Feb 19 09:53:14 2013 From: nickengland at gmail.com (Nick England) Date: Tue, 19 Feb 2013 09:53:14 +0000 Subject: [Biojava-l] Reading SCF files In-Reply-To: References: Message-ID: I get the same error message, it looks like a bug in BioJava parsing comments from SCF files. My SCF files load fine, but they don't have comments inside. Has anyone else seen this problem before? - Nick On 18 February 2013 19:48, Janier J. Ram?rez wrote: > Traying to read this SCF file, I get the following errors and warnings, > the fail is at: > > Chromatogram scf = ChromatogramFactory.create(stream); > > Warning: the code set (2) is not specifically supported. (It may still > work, though.) > Exception in thread "main" java.lang.IllegalArgumentException: Can't skip > backwards: (newOffset==0) < (offset==128) > at org.biojava.bio.program.scf.SCF$Parser.skipTo(SCF.java:424) > at > org.biojava.bio.program.scf.SCF$Parser.parseComments(SCF.java:384) > at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:372) > at > org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:206) > at org.biojava.bio.program.scf.SCF.load(SCF.java:149) > at org.biojava.bio.program.scf.SCF.create(SCF.java:133) > at > org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:117) > at javaapplication1.NewClass.main(NewClass.java:44) > > > And this is my code > > public class NewClass { > > public static void main(String[] args) > throws Exception { > JFileChooser fileChooser = new JFileChooser(); > fileChooser.setDialogTitle("Abrir"); > fileChooser.setMultiSelectionEnabled(true); > > int a = JFileChooser.APPROVE_OPTION; > > fileChooser.setFileFilter(new Filtro("scf", "")); > if (a == fileChooser.showOpenDialog(null)) { > > File file = fileChooser.getSelectedFile(); > InputStream stream = new FileInputStream(file); > > Chromatogram scf = ChromatogramFactory.create(stream); > /***Here is the fail***/ > > stream.close(); > Alignment data = scf.getBaseCalls(); > String seq = data.symbolListForLabel("dna").seqString(); > } > > } > } > > Thanks > > ----- Mensaje original ----- > De: "Nick England" > Para: "Janier J. Ram?rez" > CC: biojava-l at lists.open-bio.org > Enviados: Lunes, 18 de Febrero 2013 5:13:12 > Asunto: Re: [Biojava-l] Reading SCF files > > Janier, > > Here is a snippet which should read in SCF files for you, you will have to > have BioJava 1.0 for this to work. > > File file = new File(String "your path here"); > InputStream stream = new FileInputStream(file); > Chromatogram scf= ChromatogramFactory.create(stream); > stream.close(); > Alignment data = scf.getBaseCalls(); > String seq=data.symbolListForLabel("dna").seqString(); > > Cheers, > > Nick > > > > On 18 February 2013 05:09, Janier J. Ram?rez < > jjramirez at estudiantes.uci.cu > wrote: > > > Yes that's ok, Now I need an example of how given the path of the scf > file, get the secuence, to them parse it to fasta, or if I can do it > directly from scf to fasta. > > Thanks for your time > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > > From radomir.adamek at hotmail.com Tue Feb 19 10:08:44 2013 From: radomir.adamek at hotmail.com (Radomir) Date: Tue, 19 Feb 2013 02:08:44 -0800 (PST) Subject: [Biojava-l] BioJava, oracle problem with jdk In-Reply-To: <34984653.post@talk.nabble.com> References: <34984653.post@talk.nabble.com> Message-ID: <35040465.post@talk.nabble.com> Ahh, i`m almost home. Now i have problem with 2 methods from java 1.6. In alignment package there is a 2 methods copyof() and isempty() that can`t be compile with 1.5: [ERROR] C:\Users\radamek\workspace\maven.1361187141685\biojava\biojava3-alignment\src\main\java\org\biojava3\alignment\SimpleSubstitutionMatrix.java:[145,33] cannot find symbol [ERROR] symbol : method isEmpty() [ERROR] location: class java.lang.String [ERROR] C:\Users\radamek\workspace\maven.1361187141685\biojava\biojava3-alignment\src\main\java\org\biojava3\alignment\SimpleSubstitutionMatrix.java:[185,28] cannot find symbol [ERROR] symbol : method copyOf(short[],int) [ERROR] location: class java.util.Arrays Can somebody help me?? i found that i should make new methods, i really don`t know how to do that ( i don`t know java very well..) Radomir wrote: > > Hello, i`m trying to apply my project with oracle and biojava. I`m trying > to make a database for pairwise alignment ( FATCAT or CE ). These > algorithms are in biojava3+ packages. When i`m loading jar`s to mine > database i got error ( oracle is running on 1.5 jdk and biojava 3 is > compiled on 1.6, there are no chances to upgrade jdk on oracle ).. I find > on biojava wiki that version 3.0 of biojava is running on 1.5+ but when i > loaded these version to my database there was the same error. Here is my > question - is there any chances to get biojava 3 compiled with jdk 1.5 ? ? > Sorry for my english > -- View this message in context: http://old.nabble.com/BioJava%2C-oracle-problem-with-jdk-tp34984653p35040465.html Sent from the BioJava mailing list archive at Nabble.com. From jjramirez at estudiantes.uci.cu Thu Feb 21 14:11:08 2013 From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=) Date: Thu, 21 Feb 2013 09:11:08 -0500 (EST) Subject: [Biojava-l] Bug Reading SCF files In-Reply-To: Message-ID: <6c83019b-3b8b-4942-9fb5-ec28e21ba57f@ucimail4.uci.cu> Hi comunity ! I need help reading SCF files, I have some SCF files that Biojava is unable to read, but in others tools these files open correctly. I just need to read the file and get the sequence. help please... Thanks Janier From andreas at sdsc.edu Thu Feb 21 16:05:41 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 21 Feb 2013 08:05:41 -0800 Subject: [Biojava-l] Bug Reading SCF files In-Reply-To: <6c83019b-3b8b-4942-9fb5-ec28e21ba57f@ucimail4.uci.cu> References: <6c83019b-3b8b-4942-9fb5-ec28e21ba57f@ucimail4.uci.cu> Message-ID: Hi Janier, did you try to remove the comment lines from your file? In an earlier thread that was suggested as a possible source of problems. I think we should add porting the Chromatogram parser to BioJava 3 to our open projects page... Andreas On Thu, Feb 21, 2013 at 6:11 AM, Janier J. Ram?rez < jjramirez at estudiantes.uci.cu> wrote: > Hi comunity ! > I need help reading SCF files, I have some SCF files that Biojava is > unable to read, but in others tools these files open correctly. > I just need to read the file and get the sequence. > > help please... > Thanks > > Janier > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- ----------------------------------------------------------------------- Dr. Andreas Prlic Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego (+1) 858.246.0526 ----------------------------------------------------------------------- From andreas at sdsc.edu Thu Feb 21 16:08:33 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 21 Feb 2013 08:08:33 -0800 Subject: [Biojava-l] GSOC 2013 projects Message-ID: Hi, a few people have contacted me off-list with possible ideas regarding google summer of code projects. I think it is important to move that discussion into the public. I'd suggest that people add a few lines with their ideas to the GSOC 2013 page on our wiki: http://biojava.org/wiki/Google_Summer_of_Code_2013 Andreas From andreas at sdsc.edu Thu Feb 21 16:47:35 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 21 Feb 2013 08:47:35 -0800 Subject: [Biojava-l] Bug Reading SCF files In-Reply-To: <8573827260165005279@unknownmsgid> References: <6c83019b-3b8b-4942-9fb5-ec28e21ba57f@ucimail4.uci.cu> <8573827260165005279@unknownmsgid> Message-ID: that would be great! Andreas On Thu, Feb 21, 2013 at 8:27 AM, Hannes Brandst?tter-M?ller < admin at hannes.oib.com> wrote: > I wanted to do that last year, I think. I'll take a look at it if I > can make some time after the move to github > > Sent from my mobile. Please excuse the brevity, spelling and punctuation. > > Am 21.02.2013 um 17:15 schrieb Andreas Prlic : > > > Hi Janier, > > > > did you try to remove the comment lines from your file? In an earlier > > thread that was suggested as a possible source of problems. > > > > I think we should add porting the Chromatogram parser to BioJava 3 to our > > open projects page... > > > > Andreas > > > > > > On Thu, Feb 21, 2013 at 6:11 AM, Janier J. Ram?rez < > > jjramirez at estudiantes.uci.cu> wrote: > > > >> Hi comunity ! > >> I need help reading SCF files, I have some SCF files that Biojava is > >> unable to read, but in others tools these files open correctly. > >> I just need to read the file and get the sequence. > >> > >> help please... > >> Thanks > >> > >> Janier > >> > >> _______________________________________________ > >> Biojava-l mailing list - Biojava-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > -- > > ----------------------------------------------------------------------- > > Dr. Andreas Prlic > > Senior Scientist, RCSB PDB Protein Data Bank > > University of California, San Diego > > (+1) 858.246.0526 > > ----------------------------------------------------------------------- > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > From jjramirez at estudiantes.uci.cu Thu Feb 21 19:41:14 2013 From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=) Date: Thu, 21 Feb 2013 14:41:14 -0500 (EST) Subject: [Biojava-l] Reading SCF Files In-Reply-To: <4d83136d-33ce-4922-be52-223c9e2e9e02@ucimail4.uci.cu> Message-ID: <6fafee59-8cca-4792-9e53-a977fea3e7af@ucimail4.uci.cu> Yes, I opened the file in notepad, but there are many rare characters, I don't know where are the comments, I did send you the files that I need to read. Janier -- From jeremy at lewi.us Tue Feb 26 16:14:27 2013 From: jeremy at lewi.us (Jeremy Lewi) Date: Tue, 26 Feb 2013 08:14:27 -0800 Subject: [Biojava-l] biojava, clouds, and contrail Message-ID: Hi BioJava users, I discovered BioJava the other day while looking for some java libraries to process reads. I've been working on an assembler, Contrail, http://sourceforge.net/apps/mediawiki/contrail-bio/index.php?title=Contrail, which uses map reduce. I'd like to get more involved in the bioinformatics community so I thought I'd say hello to this group. Unfortunately, when we first started coding Contrail I didn't do a proper Google search to see if their were existing libraries for things like DNA sequence manipulation we just rolled out own because it was faster. Anyways if folks want to chat more please let me know, Best J