From jimp at compbio.dundee.ac.uk Thu Oct 4 14:10:15 2007 From: jimp at compbio.dundee.ac.uk (Jim Procter) Date: Thu Oct 4 14:10:23 2007 Subject: [Jalview-discuss] Are there any Beryl users having problems with Jalview Message-ID: <4704E637.3090900@compbio.dundee.ac.uk> Hello All. A new FAQ tip is most likely to be added to the website concerning the OpenGL linux desktop that is being shipped with the latest Ubuntu distribution (and others). The problem is purely to do with Sun's Java not being compatible with Beryl but I was wondering if anyone has found any nice workarounds. I've a couple of approaches involving patching installAnywhere, using alternate linux JVMs, or running a nested Xserver (xnest). Does anyone have any other suggestions ? cheers for your attention. Jim -- ------------------------------------------------------------------- J. B. Procter (VAMSAS Project) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk From ajperry at pansapiens.com Thu Oct 4 23:05:50 2007 From: ajperry at pansapiens.com (Andrew Perry) Date: Thu Oct 4 23:06:03 2007 Subject: [Jalview-discuss] Are there any Beryl users having problems with Jalview In-Reply-To: <4704E637.3090900@compbio.dundee.ac.uk> References: <4704E637.3090900@compbio.dundee.ac.uk> Message-ID: On 10/4/07, Jim Procter wrote: > > > The problem is purely to do with Sun's Java not being compatible with > Beryl but I was wondering if anyone has found any nice workarounds. I've > a couple of approaches involving patching installAnywhere, using > alternate linux JVMs, or running a nested Xserver (xnest). Does anyone > have any other suggestions ? > > > Hi Jim & other Jalviewers, I've found problems with Java apps (including Jalview) on Ubuntu Feisty Fawn using Beryl and the Sun JVM. I haven't tested with other JVMs. My simple "workaround" is to use the beryl-manager program to switch to a different window manager (eg metacity) while I am running any graphical Java apps. The switching seems reliable in my hands, just right-click on the little gem icon in the taskbar and select the new window manager. It also works fine even if you do it after you've started the Java app. Of course, half the time I don't remember to switch Beryl back on after I'm finished with Jalview, so I must not miss the eye candy that much :) I can't remember if beryl-manager runs at login in the default Ubuntu setup, and I'm not sure what the case will be in Gutsy. Cheers, Andrew Perry -- Postdoctoral Researcher, Trevor Lithgow Lab Department of Biochemistry and Molecular Biology Bio21 Molecular Science and Biotechnology Institute 30 Flemington Road, University of Melbourne Parkville 3010, AUSTRALIA Ph: +61 3 834442298 || Email: ajperry@unimelb.edu.au ---- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.jalview.org/pipermail/jalview-discuss/attachments/20071005/94114623/attachment.htm From jimp at compbio.dundee.ac.uk Fri Oct 5 09:36:48 2007 From: jimp at compbio.dundee.ac.uk (Jim Procter) Date: Fri Oct 5 09:36:53 2007 Subject: [Jalview-discuss] Are there any Beryl users having problems with Jalview In-Reply-To: References: <4704E637.3090900@compbio.dundee.ac.uk> Message-ID: <4705F7A0.20507@compbio.dundee.ac.uk> Thanks for this advice, Andrew. There have been a cluster of help requests concerning this, and nearly everyone was using either Ubuntu Feisty. Andrew Perry wrote: > My simple "workaround" is to use the beryl-manager program to switch > to a different window manager (eg metacity) while I am running any > graphical Java apps. The switching seems reliable in my hands, just > right-click on the little gem icon in the taskbar and select the new > window manager. It also works fine even if you do it after you've > started the Java app. Of course, half the time I don't remember to > switch Beryl back on after I'm finished with Jalview, so I must not > miss the eye candy that much :) This is always going to be the best approach. Messing around with alternate JVMs are a pain, although its easy to set up a specific script to launch a program in the alternate jvm. Its also easy to set a script to launch a nested Xserver for the program, but I'm not sure if drag'n'drop will still work then. > I can't remember if beryl-manager runs at login in the default Ubuntu > setup, and I'm not sure what the case will be in Gutsy. I've heard rumours that this will be the case - and wanted to check exactly what options we should be advising anyone to do when this bug occurs. cheers right back at ya! Jim From harijay at gmail.com Tue Oct 9 18:19:07 2007 From: harijay at gmail.com (hari jayaram) Date: Tue Oct 9 18:19:22 2007 Subject: [Jalview-discuss] Hide consensus graphic but keep sequence Message-ID: Hello, Is there a way to hide the black histogram graphic showing the amount of consensus below any alignment but still keep the consensus sequence displayed in Jalview. I can only hide the consensus "group" by hiding COnsensus in Tools - preferences under the visual tab..Can I individually hide the graphic and/or text. I am using the Jalview webstart 2.3 version. Thanks Hari -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.jalview.org/pipermail/jalview-discuss/attachments/20071009/61b990dd/attachment.htm From jimp at compbio.dundee.ac.uk Wed Oct 10 08:51:23 2007 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Wed Oct 10 08:51:39 2007 Subject: [Jalview-discuss] Hide consensus graphic but keep sequence In-Reply-To: References: Message-ID: <470C847B.4090109@compbio.dundee.ac.uk> Hi Hari. hari jayaram wrote: > Is there a way to hide the black histogram graphic showing the amount of > consensus below any alignment but still keep the consensus sequence > displayed in Jalview. You can fake it by reducing the height of the annotation bar that you want to hide the histograms of by dragging the mouse with the middle button down on unix, alt and left-button on windows or mac but its otherwise not possible to actually hide the histogram but keep the histogram labels. Jim. From B.Smith at bio.gla.ac.uk Wed Oct 17 18:36:25 2007 From: B.Smith at bio.gla.ac.uk (Brian Smith) Date: Wed Oct 17 18:36:52 2007 Subject: [Jalview-discuss] Fetching sequences, URLs, Web services etc. Message-ID: Hi, As a 1.x user I really like the look of 2.3 - will be a great tool. I am having some troubles with certain features (using webstarted 2.3 on WinXP): Fetch sequences doesn't seem to work for me. Selecting Uniprot or PDB and entering known accession numbers/ids just gives me an "Error retrieving..." dialogue each time. I think I have my proxy setting correct (bare hostname & port and the web services are working now). Does this service depend on particular servers? Is there a way to get more informative debug info? Add Sequence -> URL option. Is there a way to read sequences from SRS or NCBI via this route in a format that is recognised, or is it intended more for accessing e.g. a ready formatted file on a local server? NCBI URLs complain about the format while EBI SRS URLs load garbage composed of the characters in the URL itself which seems fair enough if you're not parsing the html stuff. Web Services: was the server really down for a while this afternoon? I was getting errors on submission but seems to be working now. Thanks, Brian Smith -- Dr. Brian O. Smith ---------------------- B Smith at bio gla ac uk Division of Biochemistry & Molecular Biology, Institute Biomedical & Life Sciences, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK. Tel: 0141 330 5167/6459/3089 Fax: 0141 330 8640 From jimp at compbio.dundee.ac.uk Mon Oct 22 14:35:59 2007 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Mon Oct 22 14:36:14 2007 Subject: [Jalview-discuss] Fetching sequences, URLs, Web services etc. In-Reply-To: References: Message-ID: <471CA73F.5020902@compbio.dundee.ac.uk> Howdo, Brian - I didn't notice your email till just now. Brian Smith wrote: > As a 1.x user I really like the look of 2.3 - will be a great tool. :) > I am having some troubles with certain features (using webstarted 2.3 on > WinXP): > > Fetch sequences doesn't seem to work for me. Selecting Uniprot or PDB > and entering known accession numbers/ids just gives me an "Error > retrieving..." dialogue each time. I think I have my proxy setting > correct (bare hostname & port and the web services are working now). > Does this service depend on particular servers? Is there a way to get > more informative debug info? There is. Jalview creates a .jalview_properties file in the directory above the 'My Documents' folder. If you close Jalview, and add the line : logs.Jalview.level=DEBUG (and make sure there's a new line at the end) then much more debugging info will be generated. logs.Axis.level=INFO can also be changed to get debug information out of the SOAP services, and logs.Castor.level=INFO can be changed to DEBUG if you want excessive info on XML serialization and deserialization. You also need to have the Java Console displayed though. If you open up the Java settings control panel (you can do this by running the command javaws -viewer) and look under the Java Console settings in the 'Advanced' tab. I'd be interested to see what the errors that you observe are. I have two independent occurences of Jalview runnng on XP boxes not being able to access either the EBI services or the Jalview questionnaire service. One of these was due to an issue at the EBI - this might be occuring for you, too. > Add Sequence -> URL option. Is there a way to read sequences from SRS > or NCBI via this route in a format that is recognised, or is it intended > more for accessing e.g. a ready formatted file on a local server? In principle you should be able to construct a URL query for both SRS and NCBI that returns a sequence file in a recognised format. Try copying the URL associated with a link on the server for viewing a sequence as fasta, for instance. At the moment, jalview doesn't discard the html tags that certain servers present the flatfiles in though - so that might be the problem. You could try cut'n'paste in that case (directly into the alignment window). NCBI > URLs complain about the format while EBI SRS URLs load garbage composed > of the characters in the URL itself which seems fair enough if you're > not parsing the html stuff. You'll have to be a bit more specific with this - can you provide some urls which were giving problems ? > Web Services: was the server really down for a while this afternoon? I > was getting errors on submission but seems to be working now. There was no downtime as far as I know. Looking at the logs, there were no errors - except for some jobs that were killed because they ran for more than an hour. If these were yours then sorry - this is the policy with public jobs. What submission errors did you get ? cheers. Jim. From jimp at compbio.dundee.ac.uk Thu Oct 25 14:50:43 2007 From: jimp at compbio.dundee.ac.uk (Jim Procter) Date: Thu Oct 25 14:51:01 2007 Subject: [Jalview-discuss] Re: Error Encontered during Installation of JAL VIEW In-Reply-To: <6aa1f4730710250636n38064ea8v8663190331686eab@mail.gmail.com> References: <6aa1f4730710190602t4de3ee8yf783515fcb85d1b9@mail.gmail.com> <4718B31B.9070204@compbio.dundee.ac.uk> <6aa1f4730710212225q3e423c4l31aaeb99eb6b9b@mail.gmail.com> <6aa1f4730710250636n38064ea8v8663190331686eab@mail.gmail.com> Message-ID: <47209F33.7040702@compbio.dundee.ac.uk> Hello Vinu. I'm very glad that you are progressing with using Jalview. > i want this to embed JalView to my html page. > and i want dynamic files to be opened into that. I suggest you examine the examples and other documentation about the applet on the Jalview website: http://www.jalview.org/examples/applets.html good luck! Jim.