Not quite true. I've been using linux x86_64 version of the sun jvm 1.5 for a while now.
I do agree that it's limited to windows, linux and solaris (32 and 64 bits for all). I don't know about other jvms. I personally like 1.5 a lot, but I'm not sure if I'd force it on all biojava users. Are you talking about core features, or just nifty add- ons that can be selectively compiled using ant? Francois On Wed, 2005-15-06 at 09:36 +0800, Richard HOLLAND wrote: > Linux supports Java 1.5 but only using the Sun JDK on ia32 and AMD > Opterons. Support for other architectures on Linux (such as ia64, PPC, > or Alpha) is restricted to specialist provisions from vendors such as HP > and the open source efforts such as Blackdown JDK. At a quick check, the > Alpha is only at 1.4.2 (from HP), likewise PPC (from IBM), whereas ia64 > can run 1.5 apps using HP's JRE but no compiler yet exists for them. > There may also be some open source purists out there who object when > they can't use their favourite open source JDK any more... > > > Richard Holland > Bioinformatics Specialist > GIS extension 8199 > --------------------------------------------- > This email is confidential and may be privileged. If you are not the > intended recipient, please delete it and notify us immediately. Please > do not copy or use it for any purpose, or disclose its content to any > other person. Thank you. > --------------------------------------------- > > > > -----Original Message----- > > From: [EMAIL PROTECTED] > > [mailto:[EMAIL PROTECTED] On Behalf Of > > [EMAIL PROTECTED] > > Sent: Wednesday, June 15, 2005 9:09 AM > > To: Michael Barton > > Cc: [EMAIL PROTECTED]; BioJava-dev > > Subject: [Biojava-l] Re: [Biojava-dev] Local binary execution > > > > > > We would normally not like to use a new JDK in biojava unless > > it is well > > supported on all the OS's people are using. Having said that > > there are > > several attractive features which would make it nice to use. > > > > Is anyones current OS not supporting java 1.5? > > > > - Mark > > > > > > > > > > > > Michael Barton <[EMAIL PROTECTED]> > > Sent by: [EMAIL PROTECTED] > > 06/15/2005 02:26 AM > > > > > > To: BioJava-dev <[EMAIL PROTECTED]> > > cc: (bcc: Mark Schreiber/GP/Novartis) > > Subject: Re: [Biojava-dev] Local binary execution > > > > > > I had a look at the post you were refering to. In terms of the ant > > support for local binary execution I think it is very similar to the > > newly implemented ProcessBuilder in Java 1.5. > > This class has a similar way way of adding command line arguments to > > that of ant <exec>. > > > > The classes I'm suggesting have an enum of arguments specific to the > > application which may convienient for suppling different > > switch/argument > > pairs, as it it means that only arguments for which the binary allows > > can be supplied. > > Any errors should therefore come from incorrent argument values rather > > than incorrect arguments. If that makes sense. > > In addition the class throws an exception if the essential arguments > > required to run the search are not supplied. > > > > This means however that the classes are written in Java 1.5. > > Would this > > be a problem? > > > > > > On Thu, 2005-06-09 at 11:54 -0400, Michael Heuer wrote: > > > Hello Michael, > > > > > > Personally I think this kind of code might be better suited > > in a more > > > general library, say in an Apache Jakarta Commons project > > for example. > > > > > > In fact, there was just a proposal to pull the exec code > > out of ant into > > a > > > separate self-contained library to the commonds-dev mailing list a > > couple > > > of days ago: > > > > > > > http://tinyurl.com/9culs > > > > > > That said, this comes up quite frequently here, so perhaps > > we should > > just > > > bite the bullet and do it up right. > > > > > > michael > > > > > > > > > On Thu, 9 Jun 2005, Michael Barton wrote: > > > > > > > > > > > Hi, > > > > > > > > I'm Bioinformatics MRes student at Newcastle. I've been > > messing around > > > > with some java code to execute bioinformatics binaries. It was > > > > originally intended for blast but has also been extended > > for genewise. > > > > It takes the hassle out of using process / process > > builder a little > > bit. > > > > > > > > Use goes along the lines of something like this > > > > > > > > //Search factory for creating searches > > > > SearchFactory<BlastSearch, BlastSearchFactory.Parameter> bsf; > > > > bsf = new BlastSearchFactory(); > > > > > > > > //Paramterise with search specific variables > > > > bsf.setSearchBinaryLocation(test_data + "/blast/binary"); > > > > > > bsf.setSearchParameter(BlastSearchFactory.Parameter.blastType, > > "blastn"); > > > > bsf.setSearchParameter(BlastSearchFactory.Parameter.database, > > > > test_data + "/blast/db/sargasso"); > > > > > > > > //Create immutable search object which can be used to run mutiple > > > > searches on the same database > > > > Search<BlastSearchResult> blastSearch = bsf.getSearch(); > > > > > > > > Simple search result object which returns inputstream > > > > SearchResult sr = blastSearch.execute(new File(test_data + > > > > "/blast/query/query")); > > > > > > > > InputStream is = sr.getResultStream(); > > > > > > > > It's seems to work okay on linux, I haven't tested it on windows. > > > > > > > > There's a little bit of JavaDoc I started work on but > > it's a little > > bit > > > > messed up from where I've been changing things around. > > > > > > > > The source/jar/doc are all here. There's test cases too. > > > > > > > > http://www.students.ncl.ac.uk/michael.barton1/ > > > > > > > > Mike > > > > > > > > _______________________________________________ > > > > biojava-dev mailing list > > > > [EMAIL PROTECTED] > > > > http://biojava.org/mailman/listinfo/biojava-dev > > > > > > > > > > > _______________________________________________ > > biojava-dev mailing list > > [EMAIL PROTECTED] > > http://biojava.org/mailman/listinfo/biojava-dev > > > > > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l@biojava.org > > http://biojava.org/mailman/listinfo/biojava-l > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
