From ngsbioinformatics at gmail.com Thu May 3 13:07:54 2012 From: ngsbioinformatics at gmail.com (Ryan Golhar) Date: Thu, 3 May 2012 13:07:54 -0400 Subject: [Biojava-l] Support of VCF, GTF, etc Message-ID: Hi - I'm looking at various frameworks to work with BAM files, VCF and GTF files. There are a couple different solutions in different languages, however I'm looking for something in Java. I noticed different people have developed different packages for this, but I haven't seen anything in Biojava. Am I missing this or is it not there? From ngsbioinformatics at gmail.com Thu May 3 13:10:26 2012 From: ngsbioinformatics at gmail.com (Ryan Golhar) Date: Thu, 3 May 2012 13:10:26 -0400 Subject: [Biojava-l] Support of VCF, GTF, etc In-Reply-To: References: Message-ID: Please disregard, I spoke to soon. On Thu, May 3, 2012 at 1:07 PM, Ryan Golhar wrote: > Hi - I'm looking at various frameworks to work with BAM files, VCF and GTF > files. There are a couple different solutions in different languages, > however I'm looking for something in Java. I noticed different people have > developed different packages for this, but I haven't seen anything in > Biojava. Am I missing this or is it not there? From daniel.quest at gmail.com Thu May 3 14:19:36 2012 From: daniel.quest at gmail.com (daniel.quest at gmail.com) Date: Thu, 3 May 2012 14:19:36 -0400 Subject: [Biojava-l] Support of VCF, GTF, etc In-Reply-To: References: Message-ID: Could Picard work for you? http://picard.sourceforge.net/ Sent from my iPhone On May 3, 2012, at 1:07 PM, Ryan Golhar wrote: > Hi - I'm looking at various frameworks to work with BAM files, VCF and GTF > files. There are a couple different solutions in different languages, > however I'm looking for something in Java. I noticed different people have > developed different packages for this, but I haven't seen anything in > Biojava. Am I missing this or is it not there? > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From schmitt at med.uni-rostock.de Mon May 7 06:21:15 2012 From: schmitt at med.uni-rostock.de (Oliver Schmitt) Date: Mon, 07 May 2012 12:21:15 +0200 Subject: [Biojava-l] Similarity measures for generalized sequences Message-ID: <4FA7A21B.5000907@med.uni-rostock.de> Hi, I'm looking for a general advice regarding the comparison of sequences (S). I mean not necessarily DNA sequences, however, sequences like Region A is connected with Regions B (shortly A->B) and then a distance or similarity measure that allows to identify similiar sequences or paths. The regions are alphanumerically coded like "Bed nucleus of the stria terminalis anterior division". Given are 10^2 to 10^7 different paths, searched are all there mutual similiarities (e.g., similarity matrix) and a multivariate classificartion like a dendrogram based on a meaningful cluster analysis. Example Given: S1: A->B->C->G S2: A->B->F->G S3: A->C->B->G S4: A->B->D->G Searched: Similiarity matrix S1 S2 S3 S4 S1 ? ? ? ? S2 ? ? ? ? S3 ? ? ? ? S4 ? ? ? ? Then I would like to generate a dendrogram based on similarity measure: S1-- |-- S2-- | |---- S3-- | |-- | S4-- Thanks a lot for any advices. Regards, Oliver -------------- next part -------------- A non-text attachment was scrubbed... Name: schmitt.vcf Type: text/x-vcard Size: 310 bytes Desc: not available URL: From andreas at sdsc.edu Mon May 7 22:33:33 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 7 May 2012 19:33:33 -0700 Subject: [Biojava-l] Similarity measures for generalized sequences In-Reply-To: <4FA7A21B.5000907@med.uni-rostock.de> References: <4FA7A21B.5000907@med.uni-rostock.de> Message-ID: Hi Oliver, Here just a couple of keywords for you to look at, not sure if you have looked at any of these already... - distance between sequences - probabilistic similarity measures - multidimensional scaling Hope that makes some sense... Andreas On Mon, May 7, 2012 at 3:21 AM, Oliver Schmitt wrote: > Hi, > > I'm looking for a general advice regarding the comparison of sequences > (S). I mean not necessarily DNA sequences, however, > sequences like Region A is connected with Regions B (shortly A->B) and > then a distance or similarity measure that > allows to identify similiar sequences or paths. The regions are > alphanumerically coded like "Bed nucleus of the stria terminalis > anterior division". > Given are 10^2 to 10^7 different paths, searched are all there mutual > similiarities (e.g., similarity matrix) and a multivariate > classificartion like a dendrogram > based on a meaningful cluster analysis. > > Example > Given: > S1: A->B->C->G > S2: A->B->F->G > S3: A->C->B->G > S4: A->B->D->G > > Searched: > Similiarity matrix > > ? ? S1 ?S2 ?S3 ?S4 > S1 ?? ? ?? ? ?? ? ?? > S2 ?? ? ?? ? ?? ? ?? > S3 ?? ? ?? ? ?? ? ?? > S4 ?? ? ?? ? ?? ? ?? > > Then I would like to generate a dendrogram based on similarity measure: > > S1-- > ? ? ? ?|-- > S2-- ? ? | > ? ? ? ? ? ? |---- > S3-- ? ? | > ? ? ? ?|-- | > S4-- > > > Thanks a lot for any advices. > > Regards, > Oliver > > _______________________________________________ > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From mictadlo at gmail.com Tue May 8 23:45:46 2012 From: mictadlo at gmail.com (Mic) Date: Wed, 9 May 2012 13:45:46 +1000 Subject: [Biojava-l] read fasta entry by entry Message-ID: Hello, I have found this http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite example, but it looks like that the whole fasta file is stored in memory. Is it possible to read any fasta entry by entry i.e. without to specify whether it is DNA/Protein? Thank you in advance. Mic From HWillis at scripps.edu Wed May 9 07:02:43 2012 From: HWillis at scripps.edu (Scooter Willis) Date: Wed, 9 May 2012 07:02:43 -0400 Subject: [Biojava-l] read fasta entry by entry In-Reply-To: Message-ID: Mic You can use the following where you set lazyloadsequences = true and the file will be indexed by the accession id in the fasta file. When you retrieve the sequence the underlying storage proxy framework knows the location of the string in the file based on its offset and will load it. Similar concept if the sequence and meta data was located at NCBI or Uniprot where we have different storage proxies that know how to get the data when it is needed. LinkedHashMap dnaSequenceList = FastaReaderHelper.readFastaDNASequence(fastaSequenceFile,lazyloadsequences); Since the objects that need to be returned from the method call are specific to the data type DNASequence vs ProteinSequence it is expected that you what is in the file. DNASequence and ProteinSequence all extend from the same parent class typical use case is that you are writing a program specific to a data type. We should probably add a feature where you can ask isProteinSequence or isDNASequence of the file etc. Thanks Scooter On 5/8/12 11:45 PM, "Mic" > wrote: Hello, I have found this http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite example, but it looks like that the whole fasta file is stored in memory. Is it possible to read any fasta entry by entry i.e. without to specify whether it is DNA/Protein? Thank you in advance. Mic _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From to.petr at gmail.com Wed May 9 19:41:44 2012 From: to.petr at gmail.com (P. Troshin) Date: Thu, 10 May 2012 00:41:44 +0100 Subject: [Biojava-l] Fwd: read fasta entry by entry In-Reply-To: References: Message-ID: Hi, Try SequenceUtil.readFasta(InputStream in). It would read sequences regardless of the type. This is a small tool in the disorder predictor package. Hope that helps, Regards, Peter On 9 May 2012 04:45, Mic wrote: > Hello, > I have found this > http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite example, but > it looks like that the whole fasta file is stored in memory. > > Is it possible to read any fasta entry by entry i.e. without > to specify whether it is DNA/Protein? > > Thank you in advance. > > Mic > _______________________________________________ > 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 Thu May 10 17:50:52 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 10 May 2012 14:50:52 -0700 Subject: [Biojava-l] biojava and Java version Message-ID: Hi, After some discussions with a user I was reminded of the issue that there are some PowerPC based OSX systems that are locked into OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java 1.6 because none of these are available for PowerPCs. While that is not our fault, the question is if we should try to make BioJava backwards compatible towards 1.5. Anybody out there on such a system? Any opinions on making BioJava java 1.5 backwards compatible again? Essentially it means a global replace all "@Override" with "" Andreas From darnells at dnastar.com Thu May 10 19:08:40 2012 From: darnells at dnastar.com (Steve Darnell) Date: Thu, 10 May 2012 23:08:40 +0000 Subject: [Biojava-l] biojava and Java version In-Reply-To: References: Message-ID: Greetings, I agree with the original BioJava3 design principles (http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 (BJ3) will freely incorporate features from Java 6." Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled for November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). Apple stopped using PowerPC processors in 2006 and has not updated OS X 10.5 in almost a year (June 2011). I suggest planning for the future rather than clinging to the past. There is a positive buzz with my coworkers about switching to Java 7. The language changes alone are a very welcomed improvement: http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html * Binary Literals * Strings in switch Statements * The try-with-resources Statement * Catching Multiple Exception Types and Rethrowing Exceptions with Improved Type Checking * Underscores in Numeric Literals * Type Inference for Generic Instance Creation * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal Parameters with Varargs Methods I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable solution for running BioJava3 on Leopard PPC? http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2. Best regards, Steve -----Original Message----- From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic Sent: Thursday, May 10, 2012 4:51 PM To: Biojava Subject: [Biojava-l] biojava and Java version Hi, After some discussions with a user I was reminded of the issue that there are some PowerPC based OSX systems that are locked into OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java 1.6 because none of these are available for PowerPCs. While that is not our fault, the question is if we should try to make BioJava backwards compatible towards 1.5. Anybody out there on such a system? Any opinions on making BioJava java 1.5 backwards compatible again? Essentially it means a global replace all "@Override" with "" Andreas _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From sbliven at ucsd.edu Thu May 10 19:29:15 2012 From: sbliven at ucsd.edu (Spencer Bliven) Date: Thu, 10 May 2012 16:29:15 -0700 Subject: [Biojava-l] biojava and Java version In-Reply-To: References: Message-ID: I see two reasons for using the @Override annotation: preventing errors in the method signature, and documenting the subclass. In practice, most of my @Overrides are added automatically by eclipse for method generation. In this case, the method signature is known to be correct, and a @see javadoc tag is automatically generated to document the connection with the superclass. Thus, I would be fine with removing all @Overrides of interface methods (which cause errors in 1.5), and probably with all @Overrides entirely. Are there any other ways we rely on 1.6? I don't think we're using the compiler library or scripting language support. Most of 1.6 is just back-end improvements. In principle I agree with Steve about moving forward. However, it looks like 1.7 will be impractical for some time (no easy OSX 10.6 support, for instance). If we're not using any 1.6 features (besides interface @Override) and we're not prepared to upgrade to 1.7, we should try to help out users with only Java 5. -Spencer On Thu, May 10, 2012 at 2:50 PM, Andreas Prlic wrote: > Hi, > > After some discussions with a user I was reminded of the issue that > there are some PowerPC based OSX systems that are locked into > OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java > 1.6 because none of these are available for PowerPCs. While that is > not our fault, the question is if we should try to make BioJava > backwards compatible towards 1.5. > > Anybody out there on such a system? > > Any opinions on making BioJava java 1.5 backwards compatible again? > Essentially it means a global replace all "@Override" with "" > > Andreas > _______________________________________________ > 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 Thu May 10 20:08:53 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Fri, 11 May 2012 00:08:53 +0000 Subject: [Biojava-l] biojava and Java version In-Reply-To: References: Message-ID: Hi Steve, I agree with looking forward and I usually give the EOL argument to Java 1.5 users as well and try to convince them to upgrade, too. In the end Apple is to blame for putting this customer in a difficult situation and not having the choice of an upgrade. I am bringing this up since at the RCSB PDB we are using BioJava in a couple of Java webstart applications and as such we are confronted with a diverse user group. 80% of the users are on Java 1.6, but the rest is using a variety of newer and older versions. Since we can't control the Java version at the user end I would prefer to stay a bit backwards compatible as long as it does not cause pain and move along with the bulk of users. Removing @Override annotations seems like an easy enough compromise for supporting 1.5 and making the few people happy, who are still stuck with legacy hardware. Andreas On Thu, May 10, 2012 at 4:08 PM, Steve Darnell wrote: > Greetings, > > I agree with the original BioJava3 design principles (http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 (BJ3) will freely incorporate features from Java 6." > > Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled for November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). Apple stopped using PowerPC processors in 2006 and has not updated OS X 10.5 in almost a year (June 2011). > > I suggest planning for the future rather than clinging to the past. There is a positive buzz with my coworkers about switching to Java 7. The language changes alone are a very welcomed improvement: http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html > > * Binary Literals > * Strings in switch Statements > * The try-with-resources Statement > * Catching Multiple Exception Types and Rethrowing Exceptions with Improved Type Checking > * Underscores in Numeric Literals > * Type Inference for Generic Instance Creation > * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal Parameters with Varargs Methods > > I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable solution for running BioJava3 on Leopard PPC? http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2. > > Best regards, > Steve > > -----Original Message----- > From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic > Sent: Thursday, May 10, 2012 4:51 PM > To: Biojava > Subject: [Biojava-l] biojava and Java version > > Hi, > > After some discussions with a user I was reminded of the issue that there are some PowerPC based OSX systems that are locked into > OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java > 1.6 because none of these are available for PowerPCs. While that is not our fault, the question is if we should try to make BioJava backwards compatible towards 1.5. > > Anybody out there on such a system? > > Any opinions on making BioJava java 1.5 backwards compatible again? > Essentially it means a global replace all "@Override" with "" > > Andreas > _______________________________________________ > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From mictadlo at gmail.com Thu May 10 22:15:05 2012 From: mictadlo at gmail.com (Mic) Date: Fri, 11 May 2012 12:15:05 +1000 Subject: [Biojava-l] biojava and Java version In-Reply-To: References: Message-ID: Apple joined OpenJDK http://openjdk.java.net/projects/macosx-port/ . On Fri, May 11, 2012 at 10:08 AM, Andreas Prlic wrote: > Hi Steve, > > I agree with looking forward and I usually give the EOL argument to > Java 1.5 users as well and try to convince them to upgrade, too. In > the end Apple is to blame for putting this customer in a difficult > situation and not having the choice of an upgrade. > > I am bringing this up since at the RCSB PDB we are using BioJava in a > couple of Java webstart applications and as such we are confronted > with a diverse user group. 80% of the users are on Java 1.6, but the > rest is using a variety of newer and older versions. > > Since we can't control the Java version at the user end I would prefer > to stay a bit backwards compatible as long as it does not cause pain > and move along with the bulk of users. Removing @Override annotations > seems like an easy enough compromise for supporting 1.5 and making the > few people happy, who are still stuck with legacy hardware. > > Andreas > > > > > > On Thu, May 10, 2012 at 4:08 PM, Steve Darnell > wrote: > > Greetings, > > > > I agree with the original BioJava3 design principles ( > http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 > (BJ3) will freely incorporate features from Java 6." > > > > Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled for > November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). > Apple stopped using PowerPC processors in 2006 and has not updated OS X > 10.5 in almost a year (June 2011). > > > > I suggest planning for the future rather than clinging to the past. > There is a positive buzz with my coworkers about switching to Java 7. The > language changes alone are a very welcomed improvement: > http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html > > > > * Binary Literals > > * Strings in switch Statements > > * The try-with-resources Statement > > * Catching Multiple Exception Types and Rethrowing Exceptions with > Improved Type Checking > > * Underscores in Numeric Literals > > * Type Inference for Generic Instance Creation > > * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal > Parameters with Varargs Methods > > > > I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. > Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable > solution for running BioJava3 on Leopard PPC? > http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2 > . > > > > Best regards, > > Steve > > > > -----Original Message----- > > From: biojava-l-bounces at lists.open-bio.org [mailto: > biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic > > Sent: Thursday, May 10, 2012 4:51 PM > > To: Biojava > > Subject: [Biojava-l] biojava and Java version > > > > Hi, > > > > After some discussions with a user I was reminded of the issue that > there are some PowerPC based OSX systems that are locked into > > OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java > > 1.6 because none of these are available for PowerPCs. While that is not > our fault, the question is if we should try to make BioJava backwards > compatible towards 1.5. > > > > Anybody out there on such a system? > > > > Any opinions on making BioJava java 1.5 backwards compatible again? > > Essentially it means a global replace all "@Override" with "" > > > > Andreas > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > > _______________________________________________ > 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 Fri May 11 00:00:34 2012 From: darnells at dnastar.com (Steve Darnell) Date: Fri, 11 May 2012 04:00:34 +0000 Subject: [Biojava-l] biojava and Java version In-Reply-To: References: , Message-ID: Hi Andreas, In the end, we all have to make decisions that best support our users. Owning an old Mac is a tough proposition (especially a PPC in an Intel world) since the Mac culture favors OS and hardware upgrades every 2-3 years. It's easy to be left in the dust. ~Steve Sent from my HTC Merge -----Original Message----- From: Andreas Prlic [andreas at sdsc.edu] Received: Thursday, 10 May 2012, 7:08pm To: Steve Darnell [darnells at dnastar.com] CC: Biojava [biojava-l at lists.open-bio.org] Subject: Re: [Biojava-l] biojava and Java version Hi Steve, I agree with looking forward and I usually give the EOL argument to Java 1.5 users as well and try to convince them to upgrade, too. In the end Apple is to blame for putting this customer in a difficult situation and not having the choice of an upgrade. I am bringing this up since at the RCSB PDB we are using BioJava in a couple of Java webstart applications and as such we are confronted with a diverse user group. 80% of the users are on Java 1.6, but the rest is using a variety of newer and older versions. Since we can't control the Java version at the user end I would prefer to stay a bit backwards compatible as long as it does not cause pain and move along with the bulk of users. Removing @Override annotations seems like an easy enough compromise for supporting 1.5 and making the few people happy, who are still stuck with legacy hardware. Andreas On Thu, May 10, 2012 at 4:08 PM, Steve Darnell wrote: > Greetings, > > I agree with the original BioJava3 design principles (http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 (BJ3) will freely incorporate features from Java 6." > > Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled for November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). Apple stopped using PowerPC processors in 2006 and has not updated OS X 10.5 in almost a year (June 2011). > > I suggest planning for the future rather than clinging to the past. There is a positive buzz with my coworkers about switching to Java 7. The language changes alone are a very welcomed improvement: http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html > > * Binary Literals > * Strings in switch Statements > * The try-with-resources Statement > * Catching Multiple Exception Types and Rethrowing Exceptions with Improved Type Checking > * Underscores in Numeric Literals > * Type Inference for Generic Instance Creation > * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal Parameters with Varargs Methods > > I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable solution for running BioJava3 on Leopard PPC? http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2. > > Best regards, > Steve > > -----Original Message----- > From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic > Sent: Thursday, May 10, 2012 4:51 PM > To: Biojava > Subject: [Biojava-l] biojava and Java version > > Hi, > > After some discussions with a user I was reminded of the issue that there are some PowerPC based OSX systems that are locked into > OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java > 1.6 because none of these are available for PowerPCs. While that is not our fault, the question is if we should try to make BioJava backwards compatible towards 1.5. > > Anybody out there on such a system? > > Any opinions on making BioJava java 1.5 backwards compatible again? > Essentially it means a global replace all "@Override" with "" > > Andreas > _______________________________________________ > 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 Fri May 11 00:09:20 2012 From: darnells at dnastar.com (Steve Darnell) Date: Fri, 11 May 2012 04:09:20 +0000 Subject: [Biojava-l] biojava and Java version In-Reply-To: References: , Message-ID: Hi Mic, The current OpenJDK Java 7 Mac port requires a 64-bit Intel Mac running OS X 10.7.3. The user in question is using a 32-bit PPC Mac running OS X 10.5. Oracle does not have plans to support anything less than 10.7: https://wikis.oracle.com/display/OpenJDK/Mac+OS+X+Port+Prerequisites ~Steve Sent from my HTC Merge -----Original Message----- From: Mic [mictadlo at gmail.com] Received: Thursday, 10 May 2012, 9:15pm To: Andreas Prlic [andreas at sdsc.edu] CC: Steve Darnell [darnells at dnastar.com]; Biojava [biojava-l at lists.open-bio.org] Subject: Re: [Biojava-l] biojava and Java version Apple joined OpenJDK http://openjdk.java.net/projects/macosx-port/ . On Fri, May 11, 2012 at 10:08 AM, Andreas Prlic > wrote: Hi Steve, I agree with looking forward and I usually give the EOL argument to Java 1.5 users as well and try to convince them to upgrade, too. In the end Apple is to blame for putting this customer in a difficult situation and not having the choice of an upgrade. I am bringing this up since at the RCSB PDB we are using BioJava in a couple of Java webstart applications and as such we are confronted with a diverse user group. 80% of the users are on Java 1.6, but the rest is using a variety of newer and older versions. Since we can't control the Java version at the user end I would prefer to stay a bit backwards compatible as long as it does not cause pain and move along with the bulk of users. Removing @Override annotations seems like an easy enough compromise for supporting 1.5 and making the few people happy, who are still stuck with legacy hardware. Andreas On Thu, May 10, 2012 at 4:08 PM, Steve Darnell > wrote: > Greetings, > > I agree with the original BioJava3 design principles (http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 (BJ3) will freely incorporate features from Java 6." > > Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled for November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). Apple stopped using PowerPC processors in 2006 and has not updated OS X 10.5 in almost a year (June 2011). > > I suggest planning for the future rather than clinging to the past. There is a positive buzz with my coworkers about switching to Java 7. The language changes alone are a very welcomed improvement: http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html > > * Binary Literals > * Strings in switch Statements > * The try-with-resources Statement > * Catching Multiple Exception Types and Rethrowing Exceptions with Improved Type Checking > * Underscores in Numeric Literals > * Type Inference for Generic Instance Creation > * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal Parameters with Varargs Methods > > I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable solution for running BioJava3 on Leopard PPC? http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2. > > Best regards, > Steve > > -----Original Message----- > From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic > Sent: Thursday, May 10, 2012 4:51 PM > To: Biojava > Subject: [Biojava-l] biojava and Java version > > Hi, > > After some discussions with a user I was reminded of the issue that there are some PowerPC based OSX systems that are locked into > OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java > 1.6 because none of these are available for PowerPCs. While that is not our fault, the question is if we should try to make BioJava backwards compatible towards 1.5. > > Anybody out there on such a system? > > Any opinions on making BioJava java 1.5 backwards compatible again? > Essentially it means a global replace all "@Override" with "" > > Andreas > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From andy.law at roslin.ed.ac.uk Fri May 11 04:14:24 2012 From: andy.law at roslin.ed.ac.uk (LAW Andy) Date: Fri, 11 May 2012 09:14:24 +0100 Subject: [Biojava-l] biojava and Java version In-Reply-To: References: , Message-ID: <28BF19EE-5390-4B1A-8DED-4A4E7A0774BF@exseed.ed.ac.uk> Are we talking about *developers* or *users* here? If we're talking about users, then could we not generate alternate versions of the maven artifacts/final jars by using profiles and the compiler plugin target designation. Only if we're talking about *developers* does the source code Annotation issue arise. How many active biojava developers are there that are running on a PPC OSX system? Or have I misunderstood? On 11 May 2012, at 05:00, Steve Darnell wrote: > Hi Andreas, > > In the end, we all have to make decisions that best support our users. Owning an old Mac is a tough proposition (especially a PPC in an Intel world) since the Mac culture favors OS and hardware upgrades every 2-3 years. It's easy to be left in the dust. > > ~Steve > > Sent from my HTC Merge > > -----Original Message----- > From: Andreas Prlic [andreas at sdsc.edu] > Received: Thursday, 10 May 2012, 7:08pm > To: Steve Darnell [darnells at dnastar.com] > CC: Biojava [biojava-l at lists.open-bio.org] > Subject: Re: [Biojava-l] biojava and Java version > > Hi Steve, > > I agree with looking forward and I usually give the EOL argument to > Java 1.5 users as well and try to convince them to upgrade, too. In > the end Apple is to blame for putting this customer in a difficult > situation and not having the choice of an upgrade. > > I am bringing this up since at the RCSB PDB we are using BioJava in a > couple of Java webstart applications and as such we are confronted > with a diverse user group. 80% of the users are on Java 1.6, but the > rest is using a variety of newer and older versions. > > Since we can't control the Java version at the user end I would prefer > to stay a bit backwards compatible as long as it does not cause pain > and move along with the bulk of users. Removing @Override annotations > seems like an easy enough compromise for supporting 1.5 and making the > few people happy, who are still stuck with legacy hardware. > > Andreas > > > > > > On Thu, May 10, 2012 at 4:08 PM, Steve Darnell wrote: >> Greetings, >> >> I agree with the original BioJava3 design principles (http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 (BJ3) will freely incorporate features from Java 6." >> >> Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled for November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). Apple stopped using PowerPC processors in 2006 and has not updated OS X 10.5 in almost a year (June 2011). >> >> I suggest planning for the future rather than clinging to the past. There is a positive buzz with my coworkers about switching to Java 7. The language changes alone are a very welcomed improvement: http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html >> >> * Binary Literals >> * Strings in switch Statements >> * The try-with-resources Statement >> * Catching Multiple Exception Types and Rethrowing Exceptions with Improved Type Checking >> * Underscores in Numeric Literals >> * Type Inference for Generic Instance Creation >> * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal Parameters with Varargs Methods >> >> I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable solution for running BioJava3 on Leopard PPC? http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2. >> >> Best regards, >> Steve >> >> -----Original Message----- >> From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic >> Sent: Thursday, May 10, 2012 4:51 PM >> To: Biojava >> Subject: [Biojava-l] biojava and Java version >> >> Hi, >> >> After some discussions with a user I was reminded of the issue that there are some PowerPC based OSX systems that are locked into >> OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java >> 1.6 because none of these are available for PowerPCs. While that is not our fault, the question is if we should try to make BioJava backwards compatible towards 1.5. >> >> Anybody out there on such a system? >> >> Any opinions on making BioJava java 1.5 backwards compatible again? >> Essentially it means a global replace all "@Override" with "" >> >> Andreas >> _______________________________________________ >> Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From simon.rayner.cn at gmail.com Fri May 11 05:03:16 2012 From: simon.rayner.cn at gmail.com (simon rayner) Date: Fri, 11 May 2012 17:03:16 +0800 Subject: [Biojava-l] biojava and Java version In-Reply-To: <28BF19EE-5390-4B1A-8DED-4A4E7A0774BF@exseed.ed.ac.uk> References: <28BF19EE-5390-4B1A-8DED-4A4E7A0774BF@exseed.ed.ac.uk> Message-ID: that was what i was thinking too. people are spending gobs of cash on instrumentation, is it unreasonable to ask users to pick up a secondhand post OSX mac from ebay or steal one from the office down the hall? On Fri, May 11, 2012 at 4:14 PM, LAW Andy wrote: > Are we talking about *developers* or *users* here? > > > If we're talking about users, then could we not generate alternate > versions of the maven artifacts/final jars by using profiles and the > compiler plugin target designation. > > Only if we're talking about *developers* does the source code Annotation > issue arise. How many active biojava developers are there that are running > on a PPC OSX system? > > > Or have I misunderstood? > > > On 11 May 2012, at 05:00, Steve Darnell wrote: > > > Hi Andreas, > > > > In the end, we all have to make decisions that best support our users. > Owning an old Mac is a tough proposition (especially a PPC in an Intel > world) since the Mac culture favors OS and hardware upgrades every 2-3 > years. It's easy to be left in the dust. > > > > ~Steve > > > > Sent from my HTC Merge > > > > -----Original Message----- > > From: Andreas Prlic [andreas at sdsc.edu] > > Received: Thursday, 10 May 2012, 7:08pm > > To: Steve Darnell [darnells at dnastar.com] > > CC: Biojava [biojava-l at lists.open-bio.org] > > Subject: Re: [Biojava-l] biojava and Java version > > > > Hi Steve, > > > > I agree with looking forward and I usually give the EOL argument to > > Java 1.5 users as well and try to convince them to upgrade, too. In > > the end Apple is to blame for putting this customer in a difficult > > situation and not having the choice of an upgrade. > > > > I am bringing this up since at the RCSB PDB we are using BioJava in a > > couple of Java webstart applications and as such we are confronted > > with a diverse user group. 80% of the users are on Java 1.6, but the > > rest is using a variety of newer and older versions. > > > > Since we can't control the Java version at the user end I would prefer > > to stay a bit backwards compatible as long as it does not cause pain > > and move along with the bulk of users. Removing @Override annotations > > seems like an easy enough compromise for supporting 1.5 and making the > > few people happy, who are still stuck with legacy hardware. > > > > Andreas > > > > > > > > > > > > On Thu, May 10, 2012 at 4:08 PM, Steve Darnell > wrote: > >> Greetings, > >> > >> I agree with the original BioJava3 design principles ( > http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 > (BJ3) will freely incorporate features from Java 6." > >> > >> Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled > for November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). > Apple stopped using PowerPC processors in 2006 and has not updated OS X > 10.5 in almost a year (June 2011). > >> > >> I suggest planning for the future rather than clinging to the past. > There is a positive buzz with my coworkers about switching to Java 7. The > language changes alone are a very welcomed improvement: > http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html > >> > >> * Binary Literals > >> * Strings in switch Statements > >> * The try-with-resources Statement > >> * Catching Multiple Exception Types and Rethrowing Exceptions with > Improved Type Checking > >> * Underscores in Numeric Literals > >> * Type Inference for Generic Instance Creation > >> * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal > Parameters with Varargs Methods > >> > >> I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. > Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable > solution for running BioJava3 on Leopard PPC? > http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2 > . > >> > >> Best regards, > >> Steve > >> > >> -----Original Message----- > >> From: biojava-l-bounces at lists.open-bio.org [mailto: > biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic > >> Sent: Thursday, May 10, 2012 4:51 PM > >> To: Biojava > >> Subject: [Biojava-l] biojava and Java version > >> > >> Hi, > >> > >> After some discussions with a user I was reminded of the issue that > there are some PowerPC based OSX systems that are locked into > >> OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java > >> 1.6 because none of these are available for PowerPCs. While that is not > our fault, the question is if we should try to make BioJava backwards > compatible towards 1.5. > >> > >> Anybody out there on such a system? > >> > >> Any opinions on making BioJava java 1.5 backwards compatible again? > >> Essentially it means a global replace all "@Override" with "" > >> > >> Andreas > >> _______________________________________________ > >> Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > Later, > > Andy > -------- > Yada, yada, yada... > > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If you > have received it in error, please destroy all copies and inform the sender. > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- Simon Rayner State Key Laboratory of Virology Wuhan Institute of Virology Chinese Academy of Sciences Wuhan, Hubei 430071 P.R.China +86 (27) 87199895 (office) +86 18627113001 (cell) From sbliven at ucsd.edu Fri May 11 16:23:02 2012 From: sbliven at ucsd.edu (Spencer Bliven) Date: Fri, 11 May 2012 13:23:02 -0700 Subject: [Biojava-l] biojava and Java version In-Reply-To: <28BF19EE-5390-4B1A-8DED-4A4E7A0774BF@exseed.ed.ac.uk> References: <28BF19EE-5390-4B1A-8DED-4A4E7A0774BF@exseed.ed.ac.uk> Message-ID: We're definitely talking about users. However, the code currently does not compile using java 1.5 settings. Also, I suggest we merely comment out the @Overrides so they can be easily re-added when we eventually do require a higher java version. On Fri, May 11, 2012 at 1:14 AM, LAW Andy wrote: > Are we talking about *developers* or *users* here? > > > If we're talking about users, then could we not generate alternate > versions of the maven artifacts/final jars by using profiles and the > compiler plugin target designation. > > Only if we're talking about *developers* does the source code Annotation > issue arise. How many active biojava developers are there that are running > on a PPC OSX system? > > > Or have I misunderstood? > > > On 11 May 2012, at 05:00, Steve Darnell wrote: > > > Hi Andreas, > > > > In the end, we all have to make decisions that best support our users. > Owning an old Mac is a tough proposition (especially a PPC in an Intel > world) since the Mac culture favors OS and hardware upgrades every 2-3 > years. It's easy to be left in the dust. > > > > ~Steve > > > > Sent from my HTC Merge > > > > -----Original Message----- > > From: Andreas Prlic [andreas at sdsc.edu] > > Received: Thursday, 10 May 2012, 7:08pm > > To: Steve Darnell [darnells at dnastar.com] > > CC: Biojava [biojava-l at lists.open-bio.org] > > Subject: Re: [Biojava-l] biojava and Java version > > > > Hi Steve, > > > > I agree with looking forward and I usually give the EOL argument to > > Java 1.5 users as well and try to convince them to upgrade, too. In > > the end Apple is to blame for putting this customer in a difficult > > situation and not having the choice of an upgrade. > > > > I am bringing this up since at the RCSB PDB we are using BioJava in a > > couple of Java webstart applications and as such we are confronted > > with a diverse user group. 80% of the users are on Java 1.6, but the > > rest is using a variety of newer and older versions. > > > > Since we can't control the Java version at the user end I would prefer > > to stay a bit backwards compatible as long as it does not cause pain > > and move along with the bulk of users. Removing @Override annotations > > seems like an easy enough compromise for supporting 1.5 and making the > > few people happy, who are still stuck with legacy hardware. > > > > Andreas > > > > > > > > > > > > On Thu, May 10, 2012 at 4:08 PM, Steve Darnell > wrote: > >> Greetings, > >> > >> I agree with the original BioJava3 design principles ( > http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 > (BJ3) will freely incorporate features from Java 6." > >> > >> Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled > for November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). > Apple stopped using PowerPC processors in 2006 and has not updated OS X > 10.5 in almost a year (June 2011). > >> > >> I suggest planning for the future rather than clinging to the past. > There is a positive buzz with my coworkers about switching to Java 7. The > language changes alone are a very welcomed improvement: > http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html > >> > >> * Binary Literals > >> * Strings in switch Statements > >> * The try-with-resources Statement > >> * Catching Multiple Exception Types and Rethrowing Exceptions with > Improved Type Checking > >> * Underscores in Numeric Literals > >> * Type Inference for Generic Instance Creation > >> * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal > Parameters with Varargs Methods > >> > >> I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. > Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable > solution for running BioJava3 on Leopard PPC? > http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2 > . > >> > >> Best regards, > >> Steve > >> > >> -----Original Message----- > >> From: biojava-l-bounces at lists.open-bio.org [mailto: > biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic > >> Sent: Thursday, May 10, 2012 4:51 PM > >> To: Biojava > >> Subject: [Biojava-l] biojava and Java version > >> > >> Hi, > >> > >> After some discussions with a user I was reminded of the issue that > there are some PowerPC based OSX systems that are locked into > >> OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java > >> 1.6 because none of these are available for PowerPCs. While that is not > our fault, the question is if we should try to make BioJava backwards > compatible towards 1.5. > >> > >> Anybody out there on such a system? > >> > >> Any opinions on making BioJava java 1.5 backwards compatible again? > >> Essentially it means a global replace all "@Override" with "" > >> > >> Andreas > >> _______________________________________________ > >> Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > Later, > > Andy > -------- > Yada, yada, yada... > > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If you > have received it in error, please destroy all copies and inform the sender. > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > _______________________________________________ > 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 Fri May 11 19:03:56 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Fri, 11 May 2012 16:03:56 -0700 Subject: [Biojava-l] biojava and Java version In-Reply-To: References: <28BF19EE-5390-4B1A-8DED-4A4E7A0774BF@exseed.ed.ac.uk> Message-ID: Hi, thanks to all for the comments. To come back to my initial request, it seems nobody on the list either is an owner of a powerpc or is working with users who are using such old hardware. In the meanwhile also "my" user managed to find some newer system. I take the responses as a consensus that people prefer to move forward and nobody is keen on supporting old things. I played around a bit with Andy's idea of having alternative Maven profiles. - Eclipse did not compile with source and target set to 1.5, however when compiling from the command line it seemed to work. As such having an alternate profile that sets the build target to 1.5 might be a possible work around. For now let's keep everything the way it is (on Java 1.6). If an alternative build profile can be added without too much pain I might do that next week, but it would not influence the main build. Andreas On Fri, May 11, 2012 at 1:23 PM, Spencer Bliven wrote: > We're definitely talking about users. However, the code currently does not > compile using java 1.5 settings. > > Also, I suggest we merely comment out the @Overrides so they can be easily > re-added when we eventually do require a higher java version. > > On Fri, May 11, 2012 at 1:14 AM, LAW Andy wrote: > >> Are we talking about *developers* or *users* here? >> >> >> If we're talking about users, then could we not generate alternate >> versions of the maven artifacts/final jars by using profiles and the >> compiler plugin target designation. >> >> Only if we're talking about *developers* does the source code Annotation >> issue arise. How many active biojava developers are there that are running >> on a PPC OSX system? >> >> >> Or have I misunderstood? >> >> >> On 11 May 2012, at 05:00, Steve Darnell wrote: >> >> > Hi Andreas, >> > >> > In the end, we all have to make decisions that best support our users. >> Owning an old Mac is a tough proposition (especially a PPC in an Intel >> world) since the Mac culture favors OS and hardware upgrades every 2-3 >> years. It's easy to be left in the dust. >> > >> > ~Steve >> > >> > Sent from my HTC Merge >> > >> > -----Original Message----- >> > From: Andreas Prlic [andreas at sdsc.edu] >> > Received: Thursday, 10 May 2012, 7:08pm >> > To: Steve Darnell [darnells at dnastar.com] >> > CC: Biojava [biojava-l at lists.open-bio.org] >> > Subject: Re: [Biojava-l] biojava and Java version >> > >> > Hi Steve, >> > >> > I agree with looking forward and I usually give the EOL argument to >> > Java 1.5 users as well and try to convince them to upgrade, too. ?In >> > the end Apple is to blame for putting this customer in a difficult >> > situation and not having the choice of an upgrade. >> > >> > I am bringing this up since at the RCSB PDB we are using BioJava in a >> > couple of Java webstart applications and as such we are confronted >> > with a diverse user group. ?80% of the users are on Java 1.6, ?but the >> > rest is using a variety of newer and older versions. >> > >> > Since we can't control the Java version at the user end I would prefer >> > to stay a bit backwards compatible as long as it does not cause pain >> > and move along with the bulk of users. ?Removing @Override annotations >> > seems like an easy enough compromise for supporting 1.5 and making the >> > few people happy, who are still stuck with legacy hardware. >> > >> > Andreas >> > >> > >> > >> > >> > >> > On Thu, May 10, 2012 at 4:08 PM, Steve Darnell >> wrote: >> >> Greetings, >> >> >> >> I agree with the original BioJava3 design principles ( >> http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 >> (BJ3) will freely incorporate features from Java 6." >> >> >> >> Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled >> for November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). >> Apple stopped using PowerPC processors in 2006 and has not updated OS X >> 10.5 in almost a year (June 2011). >> >> >> >> I suggest planning for the future rather than clinging to the past. >> There is a positive buzz with my coworkers about switching to Java 7. The >> language changes alone are a very welcomed improvement: >> http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html >> >> >> >> * Binary Literals >> >> * Strings in switch Statements >> >> * The try-with-resources Statement >> >> * Catching Multiple Exception Types and Rethrowing Exceptions with >> Improved Type Checking >> >> * Underscores in Numeric Literals >> >> * Type Inference for Generic Instance Creation >> >> * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal >> Parameters with Varargs Methods >> >> >> >> I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. >> Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable >> solution for running BioJava3 on Leopard PPC? >> http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2 >> . >> >> >> >> Best regards, >> >> Steve >> >> >> >> -----Original Message----- >> >> From: biojava-l-bounces at lists.open-bio.org [mailto: >> biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic >> >> Sent: Thursday, May 10, 2012 4:51 PM >> >> To: Biojava >> >> Subject: [Biojava-l] biojava and Java version >> >> >> >> Hi, >> >> >> >> After some discussions with a user I was reminded of the issue that >> there are some PowerPC based OSX systems that are locked into >> >> OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java >> >> 1.6 because none of these are available for PowerPCs. While that is not >> our fault, the question is if we should try to make BioJava backwards >> compatible towards 1.5. >> >> >> >> Anybody out there on such a system? >> >> >> >> Any opinions on making BioJava java 1.5 backwards compatible again? >> >> Essentially it means a global replace all "@Override" with "" >> >> >> >> Andreas >> >> _______________________________________________ >> >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > >> > _______________________________________________ >> > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/biojava-l >> >> Later, >> >> Andy >> -------- >> Yada, yada, yada... >> >> The University of Edinburgh is a charitable body, registered in Scotland, >> with registration number SC005336 >> Disclaimer: This e-mail and any attachments are confidential and intended >> solely for the use of the recipient(s) to whom they are addressed. If you >> have received it in error, please destroy all copies and inform the sender. >> >> >> >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> >> _______________________________________________ >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > _______________________________________________ > 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 Fri May 11 19:10:37 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Fri, 11 May 2012 16:10:37 -0700 Subject: [Biojava-l] Fwd: read fasta entry by entry In-Reply-To: References: Message-ID: Hi Peter and Scooter, It would be great to improve the documentation for this on the wiki and to consolidate the two Fasta parsers. Peter: utility methods are better in -core, rather than in the specialized modules. They are hard to find that way and create unexpected module dependencies. Any chance to move this to the core module? Thanks, Andreas On Wed, May 9, 2012 at 4:41 PM, P. Troshin wrote: > Hi, > > Try SequenceUtil.readFasta(InputStream in). It would read sequences > regardless of the type. > This is a small tool in the disorder predictor package. > > Hope that helps, > Regards, > Peter > > > > On 9 May 2012 04:45, Mic wrote: > >> Hello, >> I have found this >> http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite example, but >> it looks like that the whole fasta file is stored in memory. >> >> Is it possible to read any fasta entry by entry i.e. without >> to specify whether it is DNA/Protein? >> >> Thank you in advance. >> >> Mic >> _______________________________________________ >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > _______________________________________________ > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From to.petr at gmail.com Sat May 12 17:51:56 2012 From: to.petr at gmail.com (P. Troshin) Date: Sat, 12 May 2012 22:51:56 +0100 Subject: [Biojava-l] Fwd: read fasta entry by entry In-Reply-To: References: Message-ID: Hi Andreas, Sorry I am a bit short of time at the moment. I think that simply moving this code into core as is is not going to help anyone, it could just cause confusion. At a very list someone need to write a bit of documentation for the users. We need to unify different BioJava FASTA parsers. I wanted to do with someone else help, within GSOC, but the project did not go ahead. So may be next year? Regards, Peter On 12 May 2012 00:10, Andreas Prlic wrote: > Hi Peter and Scooter, > > It would be great to improve the documentation for this on the wiki > and to consolidate the two Fasta parsers. Peter: utility methods are > better in -core, rather than in the specialized modules. They are hard > to find that way and create unexpected module dependencies. Any chance > to move this to the core module? > > Thanks, > > Andreas > > On Wed, May 9, 2012 at 4:41 PM, P. Troshin wrote: > > Hi, > > > > Try SequenceUtil.readFasta(InputStream in). It would read sequences > > regardless of the type. > > This is a small tool in the disorder predictor package. > > > > Hope that helps, > > Regards, > > Peter > > > > > > > > On 9 May 2012 04:45, Mic wrote: > > > >> Hello, > >> I have found this > >> http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite example, > but > >> it looks like that the whole fasta file is stored in memory. > >> > >> Is it possible to read any fasta entry by entry i.e. without > >> to specify whether it is DNA/Protein? > >> > >> Thank you in advance. > >> > >> Mic > >> _______________________________________________ > >> Biojava-l mailing list - Biojava-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > >> > > _______________________________________________ > > 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 Tue May 22 00:22:03 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 21 May 2012 21:22:03 -0700 Subject: [Biojava-l] BioJava 3.0.4 released Message-ID: BioJava 3.0.4 has been released and is available from http://www.biojava.org/wiki/BioJava:Download as well as from the BioJava maven repository at http://www.biojava.org/download/maven/ . - This is mainly a bug fix release addressing issues with the protein structure and disorder modules - One new feature: SCOP data can now be accessed from either the original SCOP site in the UK or from Berkeley (v. 1.75A) . Happy BioJava-ing, Andreas From trematodeo at gmail.com Tue May 22 09:44:20 2012 From: trematodeo at gmail.com (trematodeo at gmail.com) Date: Tue, 22 May 2012 10:44:20 -0300 Subject: [Biojava-l] What are the main pending issues or new features to be added to the BioJava? Message-ID: Hello all, I am a MSc student in bioinformatics and I have?followed?this list?for some time now?and would like to?contribute to the biojava project. Are there new modules or features to be added? Where I can find more about this? Thanks Fausto From andreas at sdsc.edu Tue May 22 14:21:43 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 22 May 2012 11:21:43 -0700 Subject: [Biojava-l] What are the main pending issues or new features to be added to the BioJava? In-Reply-To: References: Message-ID: Hi Fausto, thanks for your interest. A list of frequently requested features is at: http://biojava.org/wiki/BioJava3_Feature_Requests If you are interested in any of these we should have a quick discussion on the -dev list how to go about implementing this and getting the code hooked up... Andreas From andreas at sdsc.edu Mon May 28 13:49:55 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 28 May 2012 10:49:55 -0700 Subject: [Biojava-l] Biojava Testing and Documentation In-Reply-To: <311319073.348461338208650124.JavaMail.root@tilmb18.indiatimes.com> References: <311319073.348461338208650124.JavaMail.root@tilmb18.indiatimes.com> Message-ID: Hi Subrata, Thanks for your interest. Working with students is always a good source of feedback. Feel free to contribute as much documentation as you like on the wiki. Accounts can be created there freely. In terms of what is needed most currently, I believe we could do with some more examples for the Coobook, but also other documentation is welcome if you feel there is need for anything. http://biojava.org/wiki/BioJava:CookBook Andreas On Mon, May 28, 2012 at 5:37 AM, wrote: > Dear Dr Parlic, > > I would be happy to undertake the job of testing of some Biojava classes,documentation of those classes, or creation of manual. > > I guide students of M.Sc Bioinformatics in their 4th Semester Project, so I can undertake such things so that both students and Biojava project gets benefited mutually. > > With Regards > > Subrata Sinha > Assistant Professor > Centre for Bioinformatics Studies > Dibrugarh University > From khalil.elmazouari at gmail.com Thu May 31 09:33:28 2012 From: khalil.elmazouari at gmail.com (Khalil El Mazouari) Date: Thu, 31 May 2012 15:33:28 +0200 Subject: [Biojava-l] how to set date created on RichSequence Message-ID: <779C0BCD-A799-45EC-BD97-A865438455A3@gmail.com> Hi All, how to set a date created on RichSequence? Thanks ----- Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it. From gwaldon at geneinfinity.org Thu May 31 11:31:38 2012 From: gwaldon at geneinfinity.org (George Waldon) Date: Thu, 31 May 2012 10:31:38 -0500 Subject: [Biojava-l] how to set date created on RichSequence In-Reply-To: <779C0BCD-A799-45EC-BD97-A865438455A3@gmail.com> References: <779C0BCD-A799-45EC-BD97-A865438455A3@gmail.com> Message-ID: <20120531103138.848158x3zml80a1m@gator1273.hostgator.com> Hi Khalil, This code should set a date: RichAnnotation notes = ((RichSequence)seq).getRichAnnotation(); Date now = new Date(); SimpleDateFormat format = new SimpleDateFormat("dd-MMM-yyyy"); Note n = new SimpleNote( Terms.getDateCreatedTerm(), format.format(now).toUpperCase(), notes.getNoteSet().size()+1); notes.addNote(n); n = new SimpleNote( Terms.getDateUpdatedTerm(), format.format(now).toUpperCase(), notes.getNoteSet().size()+1); notes.addNote(n); If the notes already exist, you may have to find them and adjust the date. Best, George Quoting Khalil El Mazouari : > Hi All, > > how to set a date created on RichSequence? > > Thanks > > > > > > ----- > > Confidentiality Notice: This e-mail and any files transmitted with > it are private and confidential and are solely for the use of the > addressee. It may contain material which is legally privileged. If > you are not the addressee or the person responsible for delivering > to the addressee, please notify that you have received this e-mail > in error and that any use of it is strictly prohibited. It would be > helpful if you could notify the author by replying to it. > > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -------------------------------- George Waldon From khalil.elmazouari at gmail.com Thu May 31 13:01:37 2012 From: khalil.elmazouari at gmail.com (Khalil El Mazouari) Date: Thu, 31 May 2012 19:01:37 +0200 Subject: [Biojava-l] how to set date created on RichSequence In-Reply-To: <20120531103138.848158x3zml80a1m@gator1273.hostgator.com> References: <779C0BCD-A799-45EC-BD97-A865438455A3@gmail.com> <20120531103138.848158x3zml80a1m@gator1273.hostgator.com> Message-ID: Hi George, the dateCreated is set correctly. However, it's only printed via RichSequence.IOTools.writeEmbl and not with RichSequence.IOTools.writeGenbank!! Best khalil On 31 May 2012, at 17:31, George Waldon wrote: > Hi Khalil, > > This code should set a date: > > RichAnnotation notes = ((RichSequence)seq).getRichAnnotation(); > Date now = new Date(); > SimpleDateFormat format = new SimpleDateFormat("dd-MMM-yyyy"); > Note n = new SimpleNote( > Terms.getDateCreatedTerm(), > format.format(now).toUpperCase(), > notes.getNoteSet().size()+1); > notes.addNote(n); > n = new SimpleNote( > Terms.getDateUpdatedTerm(), > format.format(now).toUpperCase(), > notes.getNoteSet().size()+1); > notes.addNote(n); > > If the notes already exist, you may have to find them and adjust the date. > > Best, > George > > > Quoting Khalil El Mazouari : > >> Hi All, >> >> how to set a date created on RichSequence? >> >> Thanks >> >> >> >> >> >> ----- >> >> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it. >> >> >> >> >> _______________________________________________ >> Biojava-l mailing list - Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > > > -------------------------------- > George Waldon > > ----- Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it. From khalil.elmazouari at gmail.com Thu May 31 14:50:26 2012 From: khalil.elmazouari at gmail.com (Khalil El Mazouari) Date: Thu, 31 May 2012 20:50:26 +0200 Subject: [Biojava-l] RichSequence.IOTools.writeGenbank - dateCreated Message-ID: Hi, dateCreated is not printed with RichSequence.IOTools.writeGenbank !! code: Date now = new Date(); SimpleDateFormat format = new SimpleDateFormat("dd-MMM-yyyy"); SimpleNote n = new SimpleNote( Terms.getDateCreatedTerm(), format.format(now).toUpperCase(),1); seq.getNoteSet().add(n); created date is printed with writeEmbl and not writeGenbank. Best Khalil LOCUS MMU55555 334 bp mRNA linear ROD 14-SEP-2001 DEFINITION Mus musculus anti-DNA immunoglobulin heavy chain IgG mRNA, antibody 452s.11, partial cds. ACCESSION U55555 VERSION U55555.1 GI:1872430 KEYWORDS . SOURCE Mus musculus ORGANISM Mus musculus . ---- ID U55555; SV 1; linear; mRNA; STD; ROD; 334 BP. XX AC U55555; XX DT 31-MAY-2012 (Rel. 0, Created) DT 14-SEP-2001 (Rel. 0, Last updated, Version 0) XX DE Mus musculus anti-DNA immunoglobulin heavy chain IgG mRNA, antibody DE 452s.11, partial cds. XX KW . XX OS Mus musculus OC . XX ----- Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it. From ngsbioinformatics at gmail.com Thu May 3 17:07:54 2012 From: ngsbioinformatics at gmail.com (Ryan Golhar) Date: Thu, 3 May 2012 13:07:54 -0400 Subject: [Biojava-l] Support of VCF, GTF, etc Message-ID: Hi - I'm looking at various frameworks to work with BAM files, VCF and GTF files. There are a couple different solutions in different languages, however I'm looking for something in Java. I noticed different people have developed different packages for this, but I haven't seen anything in Biojava. Am I missing this or is it not there? From ngsbioinformatics at gmail.com Thu May 3 17:10:26 2012 From: ngsbioinformatics at gmail.com (Ryan Golhar) Date: Thu, 3 May 2012 13:10:26 -0400 Subject: [Biojava-l] Support of VCF, GTF, etc In-Reply-To: References: Message-ID: Please disregard, I spoke to soon. On Thu, May 3, 2012 at 1:07 PM, Ryan Golhar wrote: > Hi - I'm looking at various frameworks to work with BAM files, VCF and GTF > files. There are a couple different solutions in different languages, > however I'm looking for something in Java. I noticed different people have > developed different packages for this, but I haven't seen anything in > Biojava. Am I missing this or is it not there? From daniel.quest at gmail.com Thu May 3 18:19:36 2012 From: daniel.quest at gmail.com (daniel.quest at gmail.com) Date: Thu, 3 May 2012 14:19:36 -0400 Subject: [Biojava-l] Support of VCF, GTF, etc In-Reply-To: References: Message-ID: Could Picard work for you? http://picard.sourceforge.net/ Sent from my iPhone On May 3, 2012, at 1:07 PM, Ryan Golhar wrote: > Hi - I'm looking at various frameworks to work with BAM files, VCF and GTF > files. There are a couple different solutions in different languages, > however I'm looking for something in Java. I noticed different people have > developed different packages for this, but I haven't seen anything in > Biojava. Am I missing this or is it not there? > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From schmitt at med.uni-rostock.de Mon May 7 10:21:15 2012 From: schmitt at med.uni-rostock.de (Oliver Schmitt) Date: Mon, 07 May 2012 12:21:15 +0200 Subject: [Biojava-l] Similarity measures for generalized sequences Message-ID: <4FA7A21B.5000907@med.uni-rostock.de> Hi, I'm looking for a general advice regarding the comparison of sequences (S). I mean not necessarily DNA sequences, however, sequences like Region A is connected with Regions B (shortly A->B) and then a distance or similarity measure that allows to identify similiar sequences or paths. The regions are alphanumerically coded like "Bed nucleus of the stria terminalis anterior division". Given are 10^2 to 10^7 different paths, searched are all there mutual similiarities (e.g., similarity matrix) and a multivariate classificartion like a dendrogram based on a meaningful cluster analysis. Example Given: S1: A->B->C->G S2: A->B->F->G S3: A->C->B->G S4: A->B->D->G Searched: Similiarity matrix S1 S2 S3 S4 S1 ? ? ? ? S2 ? ? ? ? S3 ? ? ? ? S4 ? ? ? ? Then I would like to generate a dendrogram based on similarity measure: S1-- |-- S2-- | |---- S3-- | |-- | S4-- Thanks a lot for any advices. Regards, Oliver -------------- next part -------------- A non-text attachment was scrubbed... Name: schmitt.vcf Type: text/x-vcard Size: 310 bytes Desc: not available URL: From andreas at sdsc.edu Tue May 8 02:33:33 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 7 May 2012 19:33:33 -0700 Subject: [Biojava-l] Similarity measures for generalized sequences In-Reply-To: <4FA7A21B.5000907@med.uni-rostock.de> References: <4FA7A21B.5000907@med.uni-rostock.de> Message-ID: Hi Oliver, Here just a couple of keywords for you to look at, not sure if you have looked at any of these already... - distance between sequences - probabilistic similarity measures - multidimensional scaling Hope that makes some sense... Andreas On Mon, May 7, 2012 at 3:21 AM, Oliver Schmitt wrote: > Hi, > > I'm looking for a general advice regarding the comparison of sequences > (S). I mean not necessarily DNA sequences, however, > sequences like Region A is connected with Regions B (shortly A->B) and > then a distance or similarity measure that > allows to identify similiar sequences or paths. The regions are > alphanumerically coded like "Bed nucleus of the stria terminalis > anterior division". > Given are 10^2 to 10^7 different paths, searched are all there mutual > similiarities (e.g., similarity matrix) and a multivariate > classificartion like a dendrogram > based on a meaningful cluster analysis. > > Example > Given: > S1: A->B->C->G > S2: A->B->F->G > S3: A->C->B->G > S4: A->B->D->G > > Searched: > Similiarity matrix > > ? ? S1 ?S2 ?S3 ?S4 > S1 ?? ? ?? ? ?? ? ?? > S2 ?? ? ?? ? ?? ? ?? > S3 ?? ? ?? ? ?? ? ?? > S4 ?? ? ?? ? ?? ? ?? > > Then I would like to generate a dendrogram based on similarity measure: > > S1-- > ? ? ? ?|-- > S2-- ? ? | > ? ? ? ? ? ? |---- > S3-- ? ? | > ? ? ? ?|-- | > S4-- > > > Thanks a lot for any advices. > > Regards, > Oliver > > _______________________________________________ > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From mictadlo at gmail.com Wed May 9 03:45:46 2012 From: mictadlo at gmail.com (Mic) Date: Wed, 9 May 2012 13:45:46 +1000 Subject: [Biojava-l] read fasta entry by entry Message-ID: Hello, I have found this http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite example, but it looks like that the whole fasta file is stored in memory. Is it possible to read any fasta entry by entry i.e. without to specify whether it is DNA/Protein? Thank you in advance. Mic From HWillis at scripps.edu Wed May 9 11:02:43 2012 From: HWillis at scripps.edu (Scooter Willis) Date: Wed, 9 May 2012 07:02:43 -0400 Subject: [Biojava-l] read fasta entry by entry In-Reply-To: Message-ID: Mic You can use the following where you set lazyloadsequences = true and the file will be indexed by the accession id in the fasta file. When you retrieve the sequence the underlying storage proxy framework knows the location of the string in the file based on its offset and will load it. Similar concept if the sequence and meta data was located at NCBI or Uniprot where we have different storage proxies that know how to get the data when it is needed. LinkedHashMap dnaSequenceList = FastaReaderHelper.readFastaDNASequence(fastaSequenceFile,lazyloadsequences); Since the objects that need to be returned from the method call are specific to the data type DNASequence vs ProteinSequence it is expected that you what is in the file. DNASequence and ProteinSequence all extend from the same parent class typical use case is that you are writing a program specific to a data type. We should probably add a feature where you can ask isProteinSequence or isDNASequence of the file etc. Thanks Scooter On 5/8/12 11:45 PM, "Mic" > wrote: Hello, I have found this http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite example, but it looks like that the whole fasta file is stored in memory. Is it possible to read any fasta entry by entry i.e. without to specify whether it is DNA/Protein? Thank you in advance. Mic _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From to.petr at gmail.com Wed May 9 23:41:44 2012 From: to.petr at gmail.com (P. Troshin) Date: Thu, 10 May 2012 00:41:44 +0100 Subject: [Biojava-l] Fwd: read fasta entry by entry In-Reply-To: References: Message-ID: Hi, Try SequenceUtil.readFasta(InputStream in). It would read sequences regardless of the type. This is a small tool in the disorder predictor package. Hope that helps, Regards, Peter On 9 May 2012 04:45, Mic wrote: > Hello, > I have found this > http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite example, but > it looks like that the whole fasta file is stored in memory. > > Is it possible to read any fasta entry by entry i.e. without > to specify whether it is DNA/Protein? > > Thank you in advance. > > Mic > _______________________________________________ > 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 Thu May 10 21:50:52 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 10 May 2012 14:50:52 -0700 Subject: [Biojava-l] biojava and Java version Message-ID: Hi, After some discussions with a user I was reminded of the issue that there are some PowerPC based OSX systems that are locked into OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java 1.6 because none of these are available for PowerPCs. While that is not our fault, the question is if we should try to make BioJava backwards compatible towards 1.5. Anybody out there on such a system? Any opinions on making BioJava java 1.5 backwards compatible again? Essentially it means a global replace all "@Override" with "" Andreas From darnells at dnastar.com Thu May 10 23:08:40 2012 From: darnells at dnastar.com (Steve Darnell) Date: Thu, 10 May 2012 23:08:40 +0000 Subject: [Biojava-l] biojava and Java version In-Reply-To: References: Message-ID: Greetings, I agree with the original BioJava3 design principles (http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 (BJ3) will freely incorporate features from Java 6." Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled for November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). Apple stopped using PowerPC processors in 2006 and has not updated OS X 10.5 in almost a year (June 2011). I suggest planning for the future rather than clinging to the past. There is a positive buzz with my coworkers about switching to Java 7. The language changes alone are a very welcomed improvement: http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html * Binary Literals * Strings in switch Statements * The try-with-resources Statement * Catching Multiple Exception Types and Rethrowing Exceptions with Improved Type Checking * Underscores in Numeric Literals * Type Inference for Generic Instance Creation * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal Parameters with Varargs Methods I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable solution for running BioJava3 on Leopard PPC? http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2. Best regards, Steve -----Original Message----- From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic Sent: Thursday, May 10, 2012 4:51 PM To: Biojava Subject: [Biojava-l] biojava and Java version Hi, After some discussions with a user I was reminded of the issue that there are some PowerPC based OSX systems that are locked into OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java 1.6 because none of these are available for PowerPCs. While that is not our fault, the question is if we should try to make BioJava backwards compatible towards 1.5. Anybody out there on such a system? Any opinions on making BioJava java 1.5 backwards compatible again? Essentially it means a global replace all "@Override" with "" Andreas _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From sbliven at ucsd.edu Thu May 10 23:29:15 2012 From: sbliven at ucsd.edu (Spencer Bliven) Date: Thu, 10 May 2012 16:29:15 -0700 Subject: [Biojava-l] biojava and Java version In-Reply-To: References: Message-ID: I see two reasons for using the @Override annotation: preventing errors in the method signature, and documenting the subclass. In practice, most of my @Overrides are added automatically by eclipse for method generation. In this case, the method signature is known to be correct, and a @see javadoc tag is automatically generated to document the connection with the superclass. Thus, I would be fine with removing all @Overrides of interface methods (which cause errors in 1.5), and probably with all @Overrides entirely. Are there any other ways we rely on 1.6? I don't think we're using the compiler library or scripting language support. Most of 1.6 is just back-end improvements. In principle I agree with Steve about moving forward. However, it looks like 1.7 will be impractical for some time (no easy OSX 10.6 support, for instance). If we're not using any 1.6 features (besides interface @Override) and we're not prepared to upgrade to 1.7, we should try to help out users with only Java 5. -Spencer On Thu, May 10, 2012 at 2:50 PM, Andreas Prlic wrote: > Hi, > > After some discussions with a user I was reminded of the issue that > there are some PowerPC based OSX systems that are locked into > OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java > 1.6 because none of these are available for PowerPCs. While that is > not our fault, the question is if we should try to make BioJava > backwards compatible towards 1.5. > > Anybody out there on such a system? > > Any opinions on making BioJava java 1.5 backwards compatible again? > Essentially it means a global replace all "@Override" with "" > > Andreas > _______________________________________________ > 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 Fri May 11 00:08:53 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Fri, 11 May 2012 00:08:53 +0000 Subject: [Biojava-l] biojava and Java version In-Reply-To: References: Message-ID: Hi Steve, I agree with looking forward and I usually give the EOL argument to Java 1.5 users as well and try to convince them to upgrade, too. In the end Apple is to blame for putting this customer in a difficult situation and not having the choice of an upgrade. I am bringing this up since at the RCSB PDB we are using BioJava in a couple of Java webstart applications and as such we are confronted with a diverse user group. 80% of the users are on Java 1.6, but the rest is using a variety of newer and older versions. Since we can't control the Java version at the user end I would prefer to stay a bit backwards compatible as long as it does not cause pain and move along with the bulk of users. Removing @Override annotations seems like an easy enough compromise for supporting 1.5 and making the few people happy, who are still stuck with legacy hardware. Andreas On Thu, May 10, 2012 at 4:08 PM, Steve Darnell wrote: > Greetings, > > I agree with the original BioJava3 design principles (http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 (BJ3) will freely incorporate features from Java 6." > > Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled for November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). Apple stopped using PowerPC processors in 2006 and has not updated OS X 10.5 in almost a year (June 2011). > > I suggest planning for the future rather than clinging to the past. There is a positive buzz with my coworkers about switching to Java 7. The language changes alone are a very welcomed improvement: http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html > > * Binary Literals > * Strings in switch Statements > * The try-with-resources Statement > * Catching Multiple Exception Types and Rethrowing Exceptions with Improved Type Checking > * Underscores in Numeric Literals > * Type Inference for Generic Instance Creation > * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal Parameters with Varargs Methods > > I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable solution for running BioJava3 on Leopard PPC? http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2. > > Best regards, > Steve > > -----Original Message----- > From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic > Sent: Thursday, May 10, 2012 4:51 PM > To: Biojava > Subject: [Biojava-l] biojava and Java version > > Hi, > > After some discussions with a user I was reminded of the issue that there are some PowerPC based OSX systems that are locked into > OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java > 1.6 because none of these are available for PowerPCs. While that is not our fault, the question is if we should try to make BioJava backwards compatible towards 1.5. > > Anybody out there on such a system? > > Any opinions on making BioJava java 1.5 backwards compatible again? > Essentially it means a global replace all "@Override" with "" > > Andreas > _______________________________________________ > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From mictadlo at gmail.com Fri May 11 02:15:05 2012 From: mictadlo at gmail.com (Mic) Date: Fri, 11 May 2012 12:15:05 +1000 Subject: [Biojava-l] biojava and Java version In-Reply-To: References: Message-ID: Apple joined OpenJDK http://openjdk.java.net/projects/macosx-port/ . On Fri, May 11, 2012 at 10:08 AM, Andreas Prlic wrote: > Hi Steve, > > I agree with looking forward and I usually give the EOL argument to > Java 1.5 users as well and try to convince them to upgrade, too. In > the end Apple is to blame for putting this customer in a difficult > situation and not having the choice of an upgrade. > > I am bringing this up since at the RCSB PDB we are using BioJava in a > couple of Java webstart applications and as such we are confronted > with a diverse user group. 80% of the users are on Java 1.6, but the > rest is using a variety of newer and older versions. > > Since we can't control the Java version at the user end I would prefer > to stay a bit backwards compatible as long as it does not cause pain > and move along with the bulk of users. Removing @Override annotations > seems like an easy enough compromise for supporting 1.5 and making the > few people happy, who are still stuck with legacy hardware. > > Andreas > > > > > > On Thu, May 10, 2012 at 4:08 PM, Steve Darnell > wrote: > > Greetings, > > > > I agree with the original BioJava3 design principles ( > http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 > (BJ3) will freely incorporate features from Java 6." > > > > Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled for > November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). > Apple stopped using PowerPC processors in 2006 and has not updated OS X > 10.5 in almost a year (June 2011). > > > > I suggest planning for the future rather than clinging to the past. > There is a positive buzz with my coworkers about switching to Java 7. The > language changes alone are a very welcomed improvement: > http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html > > > > * Binary Literals > > * Strings in switch Statements > > * The try-with-resources Statement > > * Catching Multiple Exception Types and Rethrowing Exceptions with > Improved Type Checking > > * Underscores in Numeric Literals > > * Type Inference for Generic Instance Creation > > * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal > Parameters with Varargs Methods > > > > I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. > Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable > solution for running BioJava3 on Leopard PPC? > http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2 > . > > > > Best regards, > > Steve > > > > -----Original Message----- > > From: biojava-l-bounces at lists.open-bio.org [mailto: > biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic > > Sent: Thursday, May 10, 2012 4:51 PM > > To: Biojava > > Subject: [Biojava-l] biojava and Java version > > > > Hi, > > > > After some discussions with a user I was reminded of the issue that > there are some PowerPC based OSX systems that are locked into > > OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java > > 1.6 because none of these are available for PowerPCs. While that is not > our fault, the question is if we should try to make BioJava backwards > compatible towards 1.5. > > > > Anybody out there on such a system? > > > > Any opinions on making BioJava java 1.5 backwards compatible again? > > Essentially it means a global replace all "@Override" with "" > > > > Andreas > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > > _______________________________________________ > 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 Fri May 11 04:00:34 2012 From: darnells at dnastar.com (Steve Darnell) Date: Fri, 11 May 2012 04:00:34 +0000 Subject: [Biojava-l] biojava and Java version In-Reply-To: References: , Message-ID: Hi Andreas, In the end, we all have to make decisions that best support our users. Owning an old Mac is a tough proposition (especially a PPC in an Intel world) since the Mac culture favors OS and hardware upgrades every 2-3 years. It's easy to be left in the dust. ~Steve Sent from my HTC Merge -----Original Message----- From: Andreas Prlic [andreas at sdsc.edu] Received: Thursday, 10 May 2012, 7:08pm To: Steve Darnell [darnells at dnastar.com] CC: Biojava [biojava-l at lists.open-bio.org] Subject: Re: [Biojava-l] biojava and Java version Hi Steve, I agree with looking forward and I usually give the EOL argument to Java 1.5 users as well and try to convince them to upgrade, too. In the end Apple is to blame for putting this customer in a difficult situation and not having the choice of an upgrade. I am bringing this up since at the RCSB PDB we are using BioJava in a couple of Java webstart applications and as such we are confronted with a diverse user group. 80% of the users are on Java 1.6, but the rest is using a variety of newer and older versions. Since we can't control the Java version at the user end I would prefer to stay a bit backwards compatible as long as it does not cause pain and move along with the bulk of users. Removing @Override annotations seems like an easy enough compromise for supporting 1.5 and making the few people happy, who are still stuck with legacy hardware. Andreas On Thu, May 10, 2012 at 4:08 PM, Steve Darnell wrote: > Greetings, > > I agree with the original BioJava3 design principles (http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 (BJ3) will freely incorporate features from Java 6." > > Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled for November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). Apple stopped using PowerPC processors in 2006 and has not updated OS X 10.5 in almost a year (June 2011). > > I suggest planning for the future rather than clinging to the past. There is a positive buzz with my coworkers about switching to Java 7. The language changes alone are a very welcomed improvement: http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html > > * Binary Literals > * Strings in switch Statements > * The try-with-resources Statement > * Catching Multiple Exception Types and Rethrowing Exceptions with Improved Type Checking > * Underscores in Numeric Literals > * Type Inference for Generic Instance Creation > * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal Parameters with Varargs Methods > > I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable solution for running BioJava3 on Leopard PPC? http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2. > > Best regards, > Steve > > -----Original Message----- > From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic > Sent: Thursday, May 10, 2012 4:51 PM > To: Biojava > Subject: [Biojava-l] biojava and Java version > > Hi, > > After some discussions with a user I was reminded of the issue that there are some PowerPC based OSX systems that are locked into > OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java > 1.6 because none of these are available for PowerPCs. While that is not our fault, the question is if we should try to make BioJava backwards compatible towards 1.5. > > Anybody out there on such a system? > > Any opinions on making BioJava java 1.5 backwards compatible again? > Essentially it means a global replace all "@Override" with "" > > Andreas > _______________________________________________ > 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 Fri May 11 04:09:20 2012 From: darnells at dnastar.com (Steve Darnell) Date: Fri, 11 May 2012 04:09:20 +0000 Subject: [Biojava-l] biojava and Java version In-Reply-To: References: , Message-ID: Hi Mic, The current OpenJDK Java 7 Mac port requires a 64-bit Intel Mac running OS X 10.7.3. The user in question is using a 32-bit PPC Mac running OS X 10.5. Oracle does not have plans to support anything less than 10.7: https://wikis.oracle.com/display/OpenJDK/Mac+OS+X+Port+Prerequisites ~Steve Sent from my HTC Merge -----Original Message----- From: Mic [mictadlo at gmail.com] Received: Thursday, 10 May 2012, 9:15pm To: Andreas Prlic [andreas at sdsc.edu] CC: Steve Darnell [darnells at dnastar.com]; Biojava [biojava-l at lists.open-bio.org] Subject: Re: [Biojava-l] biojava and Java version Apple joined OpenJDK http://openjdk.java.net/projects/macosx-port/ . On Fri, May 11, 2012 at 10:08 AM, Andreas Prlic > wrote: Hi Steve, I agree with looking forward and I usually give the EOL argument to Java 1.5 users as well and try to convince them to upgrade, too. In the end Apple is to blame for putting this customer in a difficult situation and not having the choice of an upgrade. I am bringing this up since at the RCSB PDB we are using BioJava in a couple of Java webstart applications and as such we are confronted with a diverse user group. 80% of the users are on Java 1.6, but the rest is using a variety of newer and older versions. Since we can't control the Java version at the user end I would prefer to stay a bit backwards compatible as long as it does not cause pain and move along with the bulk of users. Removing @Override annotations seems like an easy enough compromise for supporting 1.5 and making the few people happy, who are still stuck with legacy hardware. Andreas On Thu, May 10, 2012 at 4:08 PM, Steve Darnell > wrote: > Greetings, > > I agree with the original BioJava3 design principles (http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 (BJ3) will freely incorporate features from Java 6." > > Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled for November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). Apple stopped using PowerPC processors in 2006 and has not updated OS X 10.5 in almost a year (June 2011). > > I suggest planning for the future rather than clinging to the past. There is a positive buzz with my coworkers about switching to Java 7. The language changes alone are a very welcomed improvement: http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html > > * Binary Literals > * Strings in switch Statements > * The try-with-resources Statement > * Catching Multiple Exception Types and Rethrowing Exceptions with Improved Type Checking > * Underscores in Numeric Literals > * Type Inference for Generic Instance Creation > * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal Parameters with Varargs Methods > > I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable solution for running BioJava3 on Leopard PPC? http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2. > > Best regards, > Steve > > -----Original Message----- > From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic > Sent: Thursday, May 10, 2012 4:51 PM > To: Biojava > Subject: [Biojava-l] biojava and Java version > > Hi, > > After some discussions with a user I was reminded of the issue that there are some PowerPC based OSX systems that are locked into > OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java > 1.6 because none of these are available for PowerPCs. While that is not our fault, the question is if we should try to make BioJava backwards compatible towards 1.5. > > Anybody out there on such a system? > > Any opinions on making BioJava java 1.5 backwards compatible again? > Essentially it means a global replace all "@Override" with "" > > Andreas > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From andy.law at roslin.ed.ac.uk Fri May 11 08:14:24 2012 From: andy.law at roslin.ed.ac.uk (LAW Andy) Date: Fri, 11 May 2012 09:14:24 +0100 Subject: [Biojava-l] biojava and Java version In-Reply-To: References: , Message-ID: <28BF19EE-5390-4B1A-8DED-4A4E7A0774BF@exseed.ed.ac.uk> Are we talking about *developers* or *users* here? If we're talking about users, then could we not generate alternate versions of the maven artifacts/final jars by using profiles and the compiler plugin target designation. Only if we're talking about *developers* does the source code Annotation issue arise. How many active biojava developers are there that are running on a PPC OSX system? Or have I misunderstood? On 11 May 2012, at 05:00, Steve Darnell wrote: > Hi Andreas, > > In the end, we all have to make decisions that best support our users. Owning an old Mac is a tough proposition (especially a PPC in an Intel world) since the Mac culture favors OS and hardware upgrades every 2-3 years. It's easy to be left in the dust. > > ~Steve > > Sent from my HTC Merge > > -----Original Message----- > From: Andreas Prlic [andreas at sdsc.edu] > Received: Thursday, 10 May 2012, 7:08pm > To: Steve Darnell [darnells at dnastar.com] > CC: Biojava [biojava-l at lists.open-bio.org] > Subject: Re: [Biojava-l] biojava and Java version > > Hi Steve, > > I agree with looking forward and I usually give the EOL argument to > Java 1.5 users as well and try to convince them to upgrade, too. In > the end Apple is to blame for putting this customer in a difficult > situation and not having the choice of an upgrade. > > I am bringing this up since at the RCSB PDB we are using BioJava in a > couple of Java webstart applications and as such we are confronted > with a diverse user group. 80% of the users are on Java 1.6, but the > rest is using a variety of newer and older versions. > > Since we can't control the Java version at the user end I would prefer > to stay a bit backwards compatible as long as it does not cause pain > and move along with the bulk of users. Removing @Override annotations > seems like an easy enough compromise for supporting 1.5 and making the > few people happy, who are still stuck with legacy hardware. > > Andreas > > > > > > On Thu, May 10, 2012 at 4:08 PM, Steve Darnell wrote: >> Greetings, >> >> I agree with the original BioJava3 design principles (http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 (BJ3) will freely incorporate features from Java 6." >> >> Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled for November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). Apple stopped using PowerPC processors in 2006 and has not updated OS X 10.5 in almost a year (June 2011). >> >> I suggest planning for the future rather than clinging to the past. There is a positive buzz with my coworkers about switching to Java 7. The language changes alone are a very welcomed improvement: http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html >> >> * Binary Literals >> * Strings in switch Statements >> * The try-with-resources Statement >> * Catching Multiple Exception Types and Rethrowing Exceptions with Improved Type Checking >> * Underscores in Numeric Literals >> * Type Inference for Generic Instance Creation >> * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal Parameters with Varargs Methods >> >> I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable solution for running BioJava3 on Leopard PPC? http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2. >> >> Best regards, >> Steve >> >> -----Original Message----- >> From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic >> Sent: Thursday, May 10, 2012 4:51 PM >> To: Biojava >> Subject: [Biojava-l] biojava and Java version >> >> Hi, >> >> After some discussions with a user I was reminded of the issue that there are some PowerPC based OSX systems that are locked into >> OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java >> 1.6 because none of these are available for PowerPCs. While that is not our fault, the question is if we should try to make BioJava backwards compatible towards 1.5. >> >> Anybody out there on such a system? >> >> Any opinions on making BioJava java 1.5 backwards compatible again? >> Essentially it means a global replace all "@Override" with "" >> >> Andreas >> _______________________________________________ >> Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From simon.rayner.cn at gmail.com Fri May 11 09:03:16 2012 From: simon.rayner.cn at gmail.com (simon rayner) Date: Fri, 11 May 2012 17:03:16 +0800 Subject: [Biojava-l] biojava and Java version In-Reply-To: <28BF19EE-5390-4B1A-8DED-4A4E7A0774BF@exseed.ed.ac.uk> References: <28BF19EE-5390-4B1A-8DED-4A4E7A0774BF@exseed.ed.ac.uk> Message-ID: that was what i was thinking too. people are spending gobs of cash on instrumentation, is it unreasonable to ask users to pick up a secondhand post OSX mac from ebay or steal one from the office down the hall? On Fri, May 11, 2012 at 4:14 PM, LAW Andy wrote: > Are we talking about *developers* or *users* here? > > > If we're talking about users, then could we not generate alternate > versions of the maven artifacts/final jars by using profiles and the > compiler plugin target designation. > > Only if we're talking about *developers* does the source code Annotation > issue arise. How many active biojava developers are there that are running > on a PPC OSX system? > > > Or have I misunderstood? > > > On 11 May 2012, at 05:00, Steve Darnell wrote: > > > Hi Andreas, > > > > In the end, we all have to make decisions that best support our users. > Owning an old Mac is a tough proposition (especially a PPC in an Intel > world) since the Mac culture favors OS and hardware upgrades every 2-3 > years. It's easy to be left in the dust. > > > > ~Steve > > > > Sent from my HTC Merge > > > > -----Original Message----- > > From: Andreas Prlic [andreas at sdsc.edu] > > Received: Thursday, 10 May 2012, 7:08pm > > To: Steve Darnell [darnells at dnastar.com] > > CC: Biojava [biojava-l at lists.open-bio.org] > > Subject: Re: [Biojava-l] biojava and Java version > > > > Hi Steve, > > > > I agree with looking forward and I usually give the EOL argument to > > Java 1.5 users as well and try to convince them to upgrade, too. In > > the end Apple is to blame for putting this customer in a difficult > > situation and not having the choice of an upgrade. > > > > I am bringing this up since at the RCSB PDB we are using BioJava in a > > couple of Java webstart applications and as such we are confronted > > with a diverse user group. 80% of the users are on Java 1.6, but the > > rest is using a variety of newer and older versions. > > > > Since we can't control the Java version at the user end I would prefer > > to stay a bit backwards compatible as long as it does not cause pain > > and move along with the bulk of users. Removing @Override annotations > > seems like an easy enough compromise for supporting 1.5 and making the > > few people happy, who are still stuck with legacy hardware. > > > > Andreas > > > > > > > > > > > > On Thu, May 10, 2012 at 4:08 PM, Steve Darnell > wrote: > >> Greetings, > >> > >> I agree with the original BioJava3 design principles ( > http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 > (BJ3) will freely incorporate features from Java 6." > >> > >> Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled > for November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). > Apple stopped using PowerPC processors in 2006 and has not updated OS X > 10.5 in almost a year (June 2011). > >> > >> I suggest planning for the future rather than clinging to the past. > There is a positive buzz with my coworkers about switching to Java 7. The > language changes alone are a very welcomed improvement: > http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html > >> > >> * Binary Literals > >> * Strings in switch Statements > >> * The try-with-resources Statement > >> * Catching Multiple Exception Types and Rethrowing Exceptions with > Improved Type Checking > >> * Underscores in Numeric Literals > >> * Type Inference for Generic Instance Creation > >> * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal > Parameters with Varargs Methods > >> > >> I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. > Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable > solution for running BioJava3 on Leopard PPC? > http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2 > . > >> > >> Best regards, > >> Steve > >> > >> -----Original Message----- > >> From: biojava-l-bounces at lists.open-bio.org [mailto: > biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic > >> Sent: Thursday, May 10, 2012 4:51 PM > >> To: Biojava > >> Subject: [Biojava-l] biojava and Java version > >> > >> Hi, > >> > >> After some discussions with a user I was reminded of the issue that > there are some PowerPC based OSX systems that are locked into > >> OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java > >> 1.6 because none of these are available for PowerPCs. While that is not > our fault, the question is if we should try to make BioJava backwards > compatible towards 1.5. > >> > >> Anybody out there on such a system? > >> > >> Any opinions on making BioJava java 1.5 backwards compatible again? > >> Essentially it means a global replace all "@Override" with "" > >> > >> Andreas > >> _______________________________________________ > >> Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > Later, > > Andy > -------- > Yada, yada, yada... > > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If you > have received it in error, please destroy all copies and inform the sender. > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- Simon Rayner State Key Laboratory of Virology Wuhan Institute of Virology Chinese Academy of Sciences Wuhan, Hubei 430071 P.R.China +86 (27) 87199895 (office) +86 18627113001 (cell) From sbliven at ucsd.edu Fri May 11 20:23:02 2012 From: sbliven at ucsd.edu (Spencer Bliven) Date: Fri, 11 May 2012 13:23:02 -0700 Subject: [Biojava-l] biojava and Java version In-Reply-To: <28BF19EE-5390-4B1A-8DED-4A4E7A0774BF@exseed.ed.ac.uk> References: <28BF19EE-5390-4B1A-8DED-4A4E7A0774BF@exseed.ed.ac.uk> Message-ID: We're definitely talking about users. However, the code currently does not compile using java 1.5 settings. Also, I suggest we merely comment out the @Overrides so they can be easily re-added when we eventually do require a higher java version. On Fri, May 11, 2012 at 1:14 AM, LAW Andy wrote: > Are we talking about *developers* or *users* here? > > > If we're talking about users, then could we not generate alternate > versions of the maven artifacts/final jars by using profiles and the > compiler plugin target designation. > > Only if we're talking about *developers* does the source code Annotation > issue arise. How many active biojava developers are there that are running > on a PPC OSX system? > > > Or have I misunderstood? > > > On 11 May 2012, at 05:00, Steve Darnell wrote: > > > Hi Andreas, > > > > In the end, we all have to make decisions that best support our users. > Owning an old Mac is a tough proposition (especially a PPC in an Intel > world) since the Mac culture favors OS and hardware upgrades every 2-3 > years. It's easy to be left in the dust. > > > > ~Steve > > > > Sent from my HTC Merge > > > > -----Original Message----- > > From: Andreas Prlic [andreas at sdsc.edu] > > Received: Thursday, 10 May 2012, 7:08pm > > To: Steve Darnell [darnells at dnastar.com] > > CC: Biojava [biojava-l at lists.open-bio.org] > > Subject: Re: [Biojava-l] biojava and Java version > > > > Hi Steve, > > > > I agree with looking forward and I usually give the EOL argument to > > Java 1.5 users as well and try to convince them to upgrade, too. In > > the end Apple is to blame for putting this customer in a difficult > > situation and not having the choice of an upgrade. > > > > I am bringing this up since at the RCSB PDB we are using BioJava in a > > couple of Java webstart applications and as such we are confronted > > with a diverse user group. 80% of the users are on Java 1.6, but the > > rest is using a variety of newer and older versions. > > > > Since we can't control the Java version at the user end I would prefer > > to stay a bit backwards compatible as long as it does not cause pain > > and move along with the bulk of users. Removing @Override annotations > > seems like an easy enough compromise for supporting 1.5 and making the > > few people happy, who are still stuck with legacy hardware. > > > > Andreas > > > > > > > > > > > > On Thu, May 10, 2012 at 4:08 PM, Steve Darnell > wrote: > >> Greetings, > >> > >> I agree with the original BioJava3 design principles ( > http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 > (BJ3) will freely incorporate features from Java 6." > >> > >> Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled > for November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). > Apple stopped using PowerPC processors in 2006 and has not updated OS X > 10.5 in almost a year (June 2011). > >> > >> I suggest planning for the future rather than clinging to the past. > There is a positive buzz with my coworkers about switching to Java 7. The > language changes alone are a very welcomed improvement: > http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html > >> > >> * Binary Literals > >> * Strings in switch Statements > >> * The try-with-resources Statement > >> * Catching Multiple Exception Types and Rethrowing Exceptions with > Improved Type Checking > >> * Underscores in Numeric Literals > >> * Type Inference for Generic Instance Creation > >> * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal > Parameters with Varargs Methods > >> > >> I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. > Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable > solution for running BioJava3 on Leopard PPC? > http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2 > . > >> > >> Best regards, > >> Steve > >> > >> -----Original Message----- > >> From: biojava-l-bounces at lists.open-bio.org [mailto: > biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic > >> Sent: Thursday, May 10, 2012 4:51 PM > >> To: Biojava > >> Subject: [Biojava-l] biojava and Java version > >> > >> Hi, > >> > >> After some discussions with a user I was reminded of the issue that > there are some PowerPC based OSX systems that are locked into > >> OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java > >> 1.6 because none of these are available for PowerPCs. While that is not > our fault, the question is if we should try to make BioJava backwards > compatible towards 1.5. > >> > >> Anybody out there on such a system? > >> > >> Any opinions on making BioJava java 1.5 backwards compatible again? > >> Essentially it means a global replace all "@Override" with "" > >> > >> Andreas > >> _______________________________________________ > >> Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > Later, > > Andy > -------- > Yada, yada, yada... > > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If you > have received it in error, please destroy all copies and inform the sender. > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > _______________________________________________ > 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 Fri May 11 23:03:56 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Fri, 11 May 2012 16:03:56 -0700 Subject: [Biojava-l] biojava and Java version In-Reply-To: References: <28BF19EE-5390-4B1A-8DED-4A4E7A0774BF@exseed.ed.ac.uk> Message-ID: Hi, thanks to all for the comments. To come back to my initial request, it seems nobody on the list either is an owner of a powerpc or is working with users who are using such old hardware. In the meanwhile also "my" user managed to find some newer system. I take the responses as a consensus that people prefer to move forward and nobody is keen on supporting old things. I played around a bit with Andy's idea of having alternative Maven profiles. - Eclipse did not compile with source and target set to 1.5, however when compiling from the command line it seemed to work. As such having an alternate profile that sets the build target to 1.5 might be a possible work around. For now let's keep everything the way it is (on Java 1.6). If an alternative build profile can be added without too much pain I might do that next week, but it would not influence the main build. Andreas On Fri, May 11, 2012 at 1:23 PM, Spencer Bliven wrote: > We're definitely talking about users. However, the code currently does not > compile using java 1.5 settings. > > Also, I suggest we merely comment out the @Overrides so they can be easily > re-added when we eventually do require a higher java version. > > On Fri, May 11, 2012 at 1:14 AM, LAW Andy wrote: > >> Are we talking about *developers* or *users* here? >> >> >> If we're talking about users, then could we not generate alternate >> versions of the maven artifacts/final jars by using profiles and the >> compiler plugin target designation. >> >> Only if we're talking about *developers* does the source code Annotation >> issue arise. How many active biojava developers are there that are running >> on a PPC OSX system? >> >> >> Or have I misunderstood? >> >> >> On 11 May 2012, at 05:00, Steve Darnell wrote: >> >> > Hi Andreas, >> > >> > In the end, we all have to make decisions that best support our users. >> Owning an old Mac is a tough proposition (especially a PPC in an Intel >> world) since the Mac culture favors OS and hardware upgrades every 2-3 >> years. It's easy to be left in the dust. >> > >> > ~Steve >> > >> > Sent from my HTC Merge >> > >> > -----Original Message----- >> > From: Andreas Prlic [andreas at sdsc.edu] >> > Received: Thursday, 10 May 2012, 7:08pm >> > To: Steve Darnell [darnells at dnastar.com] >> > CC: Biojava [biojava-l at lists.open-bio.org] >> > Subject: Re: [Biojava-l] biojava and Java version >> > >> > Hi Steve, >> > >> > I agree with looking forward and I usually give the EOL argument to >> > Java 1.5 users as well and try to convince them to upgrade, too. ?In >> > the end Apple is to blame for putting this customer in a difficult >> > situation and not having the choice of an upgrade. >> > >> > I am bringing this up since at the RCSB PDB we are using BioJava in a >> > couple of Java webstart applications and as such we are confronted >> > with a diverse user group. ?80% of the users are on Java 1.6, ?but the >> > rest is using a variety of newer and older versions. >> > >> > Since we can't control the Java version at the user end I would prefer >> > to stay a bit backwards compatible as long as it does not cause pain >> > and move along with the bulk of users. ?Removing @Override annotations >> > seems like an easy enough compromise for supporting 1.5 and making the >> > few people happy, who are still stuck with legacy hardware. >> > >> > Andreas >> > >> > >> > >> > >> > >> > On Thu, May 10, 2012 at 4:08 PM, Steve Darnell >> wrote: >> >> Greetings, >> >> >> >> I agree with the original BioJava3 design principles ( >> http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3 >> (BJ3) will freely incorporate features from Java 6." >> >> >> >> Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled >> for November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html). >> Apple stopped using PowerPC processors in 2006 and has not updated OS X >> 10.5 in almost a year (June 2011). >> >> >> >> I suggest planning for the future rather than clinging to the past. >> There is a positive buzz with my coworkers about switching to Java 7. The >> language changes alone are a very welcomed improvement: >> http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html >> >> >> >> * Binary Literals >> >> * Strings in switch Statements >> >> * The try-with-resources Statement >> >> * Catching Multiple Exception Types and Rethrowing Exceptions with >> Improved Type Checking >> >> * Underscores in Numeric Literals >> >> * Type Inference for Generic Instance Creation >> >> * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal >> Parameters with Varargs Methods >> >> >> >> I do sympathize for those who cannot upgrade from OS X 10.5 and PPC. >> Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable >> solution for running BioJava3 on Leopard PPC? >> http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2 >> . >> >> >> >> Best regards, >> >> Steve >> >> >> >> -----Original Message----- >> >> From: biojava-l-bounces at lists.open-bio.org [mailto: >> biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic >> >> Sent: Thursday, May 10, 2012 4:51 PM >> >> To: Biojava >> >> Subject: [Biojava-l] biojava and Java version >> >> >> >> Hi, >> >> >> >> After some discussions with a user I was reminded of the issue that >> there are some PowerPC based OSX systems that are locked into >> >> OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java >> >> 1.6 because none of these are available for PowerPCs. While that is not >> our fault, the question is if we should try to make BioJava backwards >> compatible towards 1.5. >> >> >> >> Anybody out there on such a system? >> >> >> >> Any opinions on making BioJava java 1.5 backwards compatible again? >> >> Essentially it means a global replace all "@Override" with "" >> >> >> >> Andreas >> >> _______________________________________________ >> >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > >> > _______________________________________________ >> > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/biojava-l >> >> Later, >> >> Andy >> -------- >> Yada, yada, yada... >> >> The University of Edinburgh is a charitable body, registered in Scotland, >> with registration number SC005336 >> Disclaimer: This e-mail and any attachments are confidential and intended >> solely for the use of the recipient(s) to whom they are addressed. If you >> have received it in error, please destroy all copies and inform the sender. >> >> >> >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> >> _______________________________________________ >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > _______________________________________________ > 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 Fri May 11 23:10:37 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Fri, 11 May 2012 16:10:37 -0700 Subject: [Biojava-l] Fwd: read fasta entry by entry In-Reply-To: References: Message-ID: Hi Peter and Scooter, It would be great to improve the documentation for this on the wiki and to consolidate the two Fasta parsers. Peter: utility methods are better in -core, rather than in the specialized modules. They are hard to find that way and create unexpected module dependencies. Any chance to move this to the core module? Thanks, Andreas On Wed, May 9, 2012 at 4:41 PM, P. Troshin wrote: > Hi, > > Try SequenceUtil.readFasta(InputStream in). It would read sequences > regardless of the type. > This is a small tool in the disorder predictor package. > > Hope that helps, > Regards, > Peter > > > > On 9 May 2012 04:45, Mic wrote: > >> Hello, >> I have found this >> http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite example, but >> it looks like that the whole fasta file is stored in memory. >> >> Is it possible to read any fasta entry by entry i.e. without >> to specify whether it is DNA/Protein? >> >> Thank you in advance. >> >> Mic >> _______________________________________________ >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > _______________________________________________ > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From to.petr at gmail.com Sat May 12 21:51:56 2012 From: to.petr at gmail.com (P. Troshin) Date: Sat, 12 May 2012 22:51:56 +0100 Subject: [Biojava-l] Fwd: read fasta entry by entry In-Reply-To: References: Message-ID: Hi Andreas, Sorry I am a bit short of time at the moment. I think that simply moving this code into core as is is not going to help anyone, it could just cause confusion. At a very list someone need to write a bit of documentation for the users. We need to unify different BioJava FASTA parsers. I wanted to do with someone else help, within GSOC, but the project did not go ahead. So may be next year? Regards, Peter On 12 May 2012 00:10, Andreas Prlic wrote: > Hi Peter and Scooter, > > It would be great to improve the documentation for this on the wiki > and to consolidate the two Fasta parsers. Peter: utility methods are > better in -core, rather than in the specialized modules. They are hard > to find that way and create unexpected module dependencies. Any chance > to move this to the core module? > > Thanks, > > Andreas > > On Wed, May 9, 2012 at 4:41 PM, P. Troshin wrote: > > Hi, > > > > Try SequenceUtil.readFasta(InputStream in). It would read sequences > > regardless of the type. > > This is a small tool in the disorder predictor package. > > > > Hope that helps, > > Regards, > > Peter > > > > > > > > On 9 May 2012 04:45, Mic wrote: > > > >> Hello, > >> I have found this > >> http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite example, > but > >> it looks like that the whole fasta file is stored in memory. > >> > >> Is it possible to read any fasta entry by entry i.e. without > >> to specify whether it is DNA/Protein? > >> > >> Thank you in advance. > >> > >> Mic > >> _______________________________________________ > >> Biojava-l mailing list - Biojava-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > >> > > _______________________________________________ > > 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 Tue May 22 04:22:03 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 21 May 2012 21:22:03 -0700 Subject: [Biojava-l] BioJava 3.0.4 released Message-ID: BioJava 3.0.4 has been released and is available from http://www.biojava.org/wiki/BioJava:Download as well as from the BioJava maven repository at http://www.biojava.org/download/maven/ . - This is mainly a bug fix release addressing issues with the protein structure and disorder modules - One new feature: SCOP data can now be accessed from either the original SCOP site in the UK or from Berkeley (v. 1.75A) . Happy BioJava-ing, Andreas From trematodeo at gmail.com Tue May 22 13:44:20 2012 From: trematodeo at gmail.com (trematodeo at gmail.com) Date: Tue, 22 May 2012 10:44:20 -0300 Subject: [Biojava-l] What are the main pending issues or new features to be added to the BioJava? Message-ID: Hello all, I am a MSc student in bioinformatics and I have?followed?this list?for some time now?and would like to?contribute to the biojava project. Are there new modules or features to be added? Where I can find more about this? Thanks Fausto From andreas at sdsc.edu Tue May 22 18:21:43 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 22 May 2012 11:21:43 -0700 Subject: [Biojava-l] What are the main pending issues or new features to be added to the BioJava? In-Reply-To: References: Message-ID: Hi Fausto, thanks for your interest. A list of frequently requested features is at: http://biojava.org/wiki/BioJava3_Feature_Requests If you are interested in any of these we should have a quick discussion on the -dev list how to go about implementing this and getting the code hooked up... Andreas From andreas at sdsc.edu Mon May 28 17:49:55 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 28 May 2012 10:49:55 -0700 Subject: [Biojava-l] Biojava Testing and Documentation In-Reply-To: <311319073.348461338208650124.JavaMail.root@tilmb18.indiatimes.com> References: <311319073.348461338208650124.JavaMail.root@tilmb18.indiatimes.com> Message-ID: Hi Subrata, Thanks for your interest. Working with students is always a good source of feedback. Feel free to contribute as much documentation as you like on the wiki. Accounts can be created there freely. In terms of what is needed most currently, I believe we could do with some more examples for the Coobook, but also other documentation is welcome if you feel there is need for anything. http://biojava.org/wiki/BioJava:CookBook Andreas On Mon, May 28, 2012 at 5:37 AM, wrote: > Dear Dr Parlic, > > I would be happy to undertake the job of testing of some Biojava classes,documentation of those classes, or creation of manual. > > I guide students of M.Sc Bioinformatics in their 4th Semester Project, so I can undertake such things so that both students and Biojava project gets benefited mutually. > > With Regards > > Subrata Sinha > Assistant Professor > Centre for Bioinformatics Studies > Dibrugarh University > From khalil.elmazouari at gmail.com Thu May 31 13:33:28 2012 From: khalil.elmazouari at gmail.com (Khalil El Mazouari) Date: Thu, 31 May 2012 15:33:28 +0200 Subject: [Biojava-l] how to set date created on RichSequence Message-ID: <779C0BCD-A799-45EC-BD97-A865438455A3@gmail.com> Hi All, how to set a date created on RichSequence? Thanks ----- Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it. From gwaldon at geneinfinity.org Thu May 31 15:31:38 2012 From: gwaldon at geneinfinity.org (George Waldon) Date: Thu, 31 May 2012 10:31:38 -0500 Subject: [Biojava-l] how to set date created on RichSequence In-Reply-To: <779C0BCD-A799-45EC-BD97-A865438455A3@gmail.com> References: <779C0BCD-A799-45EC-BD97-A865438455A3@gmail.com> Message-ID: <20120531103138.848158x3zml80a1m@gator1273.hostgator.com> Hi Khalil, This code should set a date: RichAnnotation notes = ((RichSequence)seq).getRichAnnotation(); Date now = new Date(); SimpleDateFormat format = new SimpleDateFormat("dd-MMM-yyyy"); Note n = new SimpleNote( Terms.getDateCreatedTerm(), format.format(now).toUpperCase(), notes.getNoteSet().size()+1); notes.addNote(n); n = new SimpleNote( Terms.getDateUpdatedTerm(), format.format(now).toUpperCase(), notes.getNoteSet().size()+1); notes.addNote(n); If the notes already exist, you may have to find them and adjust the date. Best, George Quoting Khalil El Mazouari : > Hi All, > > how to set a date created on RichSequence? > > Thanks > > > > > > ----- > > Confidentiality Notice: This e-mail and any files transmitted with > it are private and confidential and are solely for the use of the > addressee. It may contain material which is legally privileged. If > you are not the addressee or the person responsible for delivering > to the addressee, please notify that you have received this e-mail > in error and that any use of it is strictly prohibited. It would be > helpful if you could notify the author by replying to it. > > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -------------------------------- George Waldon From khalil.elmazouari at gmail.com Thu May 31 17:01:37 2012 From: khalil.elmazouari at gmail.com (Khalil El Mazouari) Date: Thu, 31 May 2012 19:01:37 +0200 Subject: [Biojava-l] how to set date created on RichSequence In-Reply-To: <20120531103138.848158x3zml80a1m@gator1273.hostgator.com> References: <779C0BCD-A799-45EC-BD97-A865438455A3@gmail.com> <20120531103138.848158x3zml80a1m@gator1273.hostgator.com> Message-ID: Hi George, the dateCreated is set correctly. However, it's only printed via RichSequence.IOTools.writeEmbl and not with RichSequence.IOTools.writeGenbank!! Best khalil On 31 May 2012, at 17:31, George Waldon wrote: > Hi Khalil, > > This code should set a date: > > RichAnnotation notes = ((RichSequence)seq).getRichAnnotation(); > Date now = new Date(); > SimpleDateFormat format = new SimpleDateFormat("dd-MMM-yyyy"); > Note n = new SimpleNote( > Terms.getDateCreatedTerm(), > format.format(now).toUpperCase(), > notes.getNoteSet().size()+1); > notes.addNote(n); > n = new SimpleNote( > Terms.getDateUpdatedTerm(), > format.format(now).toUpperCase(), > notes.getNoteSet().size()+1); > notes.addNote(n); > > If the notes already exist, you may have to find them and adjust the date. > > Best, > George > > > Quoting Khalil El Mazouari : > >> Hi All, >> >> how to set a date created on RichSequence? >> >> Thanks >> >> >> >> >> >> ----- >> >> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it. >> >> >> >> >> _______________________________________________ >> Biojava-l mailing list - Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > > > -------------------------------- > George Waldon > > ----- Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it. From khalil.elmazouari at gmail.com Thu May 31 18:50:26 2012 From: khalil.elmazouari at gmail.com (Khalil El Mazouari) Date: Thu, 31 May 2012 20:50:26 +0200 Subject: [Biojava-l] RichSequence.IOTools.writeGenbank - dateCreated Message-ID: Hi, dateCreated is not printed with RichSequence.IOTools.writeGenbank !! code: Date now = new Date(); SimpleDateFormat format = new SimpleDateFormat("dd-MMM-yyyy"); SimpleNote n = new SimpleNote( Terms.getDateCreatedTerm(), format.format(now).toUpperCase(),1); seq.getNoteSet().add(n); created date is printed with writeEmbl and not writeGenbank. Best Khalil LOCUS MMU55555 334 bp mRNA linear ROD 14-SEP-2001 DEFINITION Mus musculus anti-DNA immunoglobulin heavy chain IgG mRNA, antibody 452s.11, partial cds. ACCESSION U55555 VERSION U55555.1 GI:1872430 KEYWORDS . SOURCE Mus musculus ORGANISM Mus musculus . ---- ID U55555; SV 1; linear; mRNA; STD; ROD; 334 BP. XX AC U55555; XX DT 31-MAY-2012 (Rel. 0, Created) DT 14-SEP-2001 (Rel. 0, Last updated, Version 0) XX DE Mus musculus anti-DNA immunoglobulin heavy chain IgG mRNA, antibody DE 452s.11, partial cds. XX KW . XX OS Mus musculus OC . XX ----- Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.