From jimp at compbio.dundee.ac.uk Fri Aug 1 14:28:03 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Fri Aug 1 14:28:15 2008 Subject: [Jalview-discuss] sequence fetcher update Message-ID: <48930F63.5050309@compbio.dundee.ac.uk> Hi All. I've just checked in a modification to the Jalview sequence fetcher - so you can now query DAS sources that support the sequence command. This is highly experimental - let me know if you have any odd behaviour or problems (that aren't related to the DAS sources themselves... ). cheers. Jim. pps. The PFAM fetcher is still broken - I'm waiting for a recommendation from the PFAM team concerning the correct retrieval mechanism to use now they have a new SOAP API. From jimp at compbio.dundee.ac.uk Mon Aug 4 16:07:33 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Mon Aug 4 16:07:48 2008 Subject: [Jalview-discuss] sequence fetcher update In-Reply-To: <48930F63.5050309@compbio.dundee.ac.uk> References: <48930F63.5050309@compbio.dundee.ac.uk> Message-ID: <48971B35.5060209@compbio.dundee.ac.uk> Hi All. PFAM alignment retrieval has now been fixed in the development version of the Jalview Application. Jim From rkhayat at scripps.edu Tue Aug 5 19:57:32 2008 From: rkhayat at scripps.edu (Reza Khayat) Date: Tue Aug 5 19:58:36 2008 Subject: [Jalview-discuss] PDB File Message-ID: Hi, I have some threaded PDB models that Jalview will not read. The PDB format is perfectly fine, and every other program reads it. I think it has something to do with the PDB header. What needs to be in the header of a PDB file in order for Jalview to read it? If that is the problem. Regards Reza From jimp at compbio.dundee.ac.uk Tue Aug 5 20:14:33 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue Aug 5 20:14:39 2008 Subject: [Jalview-discuss] PDB File In-Reply-To: References: Message-ID: <4898A699.2010909@compbio.dundee.ac.uk> Reza Khayat wrote: > Hi, > I have some threaded PDB models that Jalview will not read. The > PDB format is perfectly fine, and every other program reads it. I think > it has something to do with the PDB header. What needs to be in the > header of a PDB file in order for Jalview to read it? If that is the > problem. This is a bug in jalview 2.3 that is fixed in the development release - have a look here: http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/latest/webstart/jalview.jnlp Jim -- ------------------------------------------------------------------- J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. From jimp at compbio.dundee.ac.uk Wed Aug 27 16:17:50 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Wed Aug 27 16:18:05 2008 Subject: [Jalview-discuss] Re: Problem when trying to start jalview from the command line in mac In-Reply-To: <3508097b0808270723u52494d8cu67872195ab023659@mail.gmail.com> References: <3508097b0808270723u52494d8cu67872195ab023659@mail.gmail.com> Message-ID: <48B5701E.6000106@compbio.dundee.ac.uk> Hi Timothy. I've cced this reply to the discuss list to see if anyone else has any ideas here. Timothy Hughes wrote: > I have some problems starting Jalview from the command line on Mac. > > Java version: 1.5.0_13 > i386 Mac OS X 10.5.4 > Jalview Version: 2.4 Thanks for trying the new version out - there are still teething problems with the release, but I'm nearly there ;) > Jalview works fine if I start it via the dock or spotlight. Ok. > But if I try to start it from the command line which is very handy in > some cases (especially when one wants to open a specific file) then I > get the following bug: > > % declare JALVIEW="/Applications/Jalview/"; > % java -Djava.ext.dirs=${JALVIEW}lib -cp ${JALVIEW}jalview.jar -Xms500M > -Xmx750M jalview.bin.Jalview -open alignment.fa > Java version: 1.5.0_13 > i386 Mac OS X 10.5.4 > Jalview Version: 2.4 > # INFO: Setting default net timeout to 30 seconds. > Opening file: alignment.fa > Exception in thread "Thread-7" java.lang.VerifyError: (class: > jalview/datamodel/Sequence, method: parseId signature: ()V) Incompatible > object argument for function call > at jalview.io.AlignFile.parseId(AlignFile.java:229) > at jalview.io.FastaFile.parse(FastaFile.java:124) > at jalview.io.AlignFile.(AlignFile.java:72) > at jalview.io.FastaFile.(FastaFile.java:59) > at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:157) > at jalview.io.FileLoader.run(FileLoader.java:272) > at java.lang.Thread.run(Thread.java:613) > error I can verify this on our own Mac, which is an earlier OSX (10.4). >From what I can tell, it is something to do with the default Java environment that is being launched from the command line. The InstallAnywhere launcher seems to be doing something additional, and its going to take a little time to track down. However, I have verified that if you build Jalview from the source distribution then it launches correctly from the command line. I am currently in the process of updating the website to reflect the new release, so for the moment, get it from http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/release/jalview-source.tar.gz Jim.