From jimp at compbio.dundee.ac.uk Tue Jul 8 09:06:13 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue Jul 8 09:06:26 2008 Subject: [Jalview-discuss] Re: how to create jalview shortcuts. In-Reply-To: <935BBB6487217A4BAC2BD26F7E024DF7071CDFDD@rnumsem03.nala.roche.com> References: <935BBB6487217A4BAC2BD26F7E024DF7071CDFDD@rnumsem03.nala.roche.com> Message-ID: <48731FF5.4060207@compbio.dundee.ac.uk> Dear Armando. It sounds like you have used the Webstart version of Jalview - which is a web based java application launch system. This is the best way to run Jalview, but it means that instead of the application being installed locally on your machine, it is 'cached' - like your web browser hangs on to a version of a page so it can be reloaded quickly. After running Jalview via webstart a few times you should be given the option of creating shortcuts, but if you want to create them right away then follow these instructions : 1. Press the start button and select the 'Run...' dialog (if you are using windows XP). 2. type javaws -viewer 3. The Java Console should appear, and after a moment, the Java Cache Viewer will also appear. In the Java Cache Viewer, look for the 'Jalview ' Application entry and right click to bring up a menu. Select the 'Install shortcuts' option, and the shortcuts will be created. If you want to find out more about webstart, there is lots of documentation on the sun web site (http://java.sun.com/j2se/1.5.0/docs/guide/javaws). happy Jalviewing. Jim Procter. Villasenor, Armando wrote: > Hello Jalview 2.3 representatives, > > > > I installed the application on my windows machine without trouble (from > your site: http://www.jalview.org/download.html. After installation the > application launched without trouble-------I was able to open some fasta > files. However, I have attempted to create a shortcut and failed. I?m > not able to create a short cut for this application--------not within > the start menu and not within the desktop. Do you have some tips on how > to create a shortcut for Jalview? > > > > Side note: > > I ran a search for Jalview in the program files folder but did not find it. > > I did not find it in the start?all programs list either. > > > > I look forward to your tips > > > > Thanks a lot, > > > > > > > -- ------------------------------------------------------------------- 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 Tue Jul 8 10:25:29 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue Jul 8 10:25:42 2008 Subject: [Jalview-discuss] Re: Problems with alignment In-Reply-To: References: Message-ID: <48733289.30000@compbio.dundee.ac.uk> Hello Shanuki - it sounds like you are experiencing network problems - either the Jalview Web services are not accessible from your local network in York, or your computer's firewall is misconfigured. Can you open these URLs in your web browser ? http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS This should have a simple HTML page returned. http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS A similar simple HTML page should be returned. http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry?method=getServices A page containing XML should be returned. If all the above work with your web browser then you probably have firewall issues - you will need to allow the Jalview application access to the network (often this means adding the java executable to the list of exceptions - programs that are allowed full access to the internet). If you don't know how to do this then contact your local network support, and show them this email. All the best - happy Jalviewing! Jim. ish500@york.ac.uk wrote: > Hi, I'm running jaliview on commmand line(linux system)and trying to > align 320 protein se4quences. Since yesterday afternoon I have trying to > align my protein sequences using options the webservice menu(Muscle > Multiple Sequence alignment, MAFFT Multiple Sequence Alignment, ClustalW > Multiple Sequence Alignment). Today morning I tried MAFFT Multiple > Sequence Alignment, ClustalW Multiple Sequence Alignment and keeps > giving the same error message.ON command lines it says : MAFFT Multiple > Sequence AlignmentClient: Failed to submit the sequences for alignment > (probably a server side problem) When contacting > Server:http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS > java.net.ConnectException: Connection timed out > > ClustalW Multiple Sequence AlignmentClient: Failed to submit the > sequences for a lignment (probably a server side problem) When > contacting > Server:http://www.compbio.dundee.ac.uk/JalviewWS/services/Clusta lWS > java.net.ConnectException: Connection timed out > > Is there any other way i could align my sequences on jaliview? > Thanking you, > Shanuki > -- ------------------------------------------------------------------- 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 paul.pillot at ac-nice.fr Tue Jul 8 13:08:32 2008 From: paul.pillot at ac-nice.fr (Paul Pillot) Date: Tue Jul 8 13:08:36 2008 Subject: [Jalview-discuss] Jalview and i18n In-Reply-To: <48733289.30000@compbio.dundee.ac.uk> References: <48733289.30000@compbio.dundee.ac.uk> Message-ID: <00A50D9B-B1A3-495B-A739-CC783CF6D006@ac-nice.fr> Hello, I am a biology teacher for secondary education in France and would like to use Jalview with my students. I was wondering if there is any plan for internationalization or if I should look into creating another Jalview version through a translation of the code ? Thank-you, Paul From jimp at compbio.dundee.ac.uk Wed Jul 9 09:37:51 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Wed Jul 9 09:38:02 2008 Subject: [Jalview-discuss] Jalview and i18n In-Reply-To: <00A50D9B-B1A3-495B-A739-CC783CF6D006@ac-nice.fr> References: <48733289.30000@compbio.dundee.ac.uk> <00A50D9B-B1A3-495B-A739-CC783CF6D006@ac-nice.fr> Message-ID: <487478DF.2010808@compbio.dundee.ac.uk> Hello Paul. Paul Pillot wrote: > I am a biology teacher for secondary education in France and would like > to use Jalview with my students. I was wondering if there is any plan > for internationalization or if I should look into creating another > Jalview version through a translation of the code ? It would be best if the Jalview source did not fork into internationalized and 'en-only' versions. However, we have not explicitly planned for internationalization but it has been requested quite frequently, and would obviously be of great benefit! Now that Jalview development is slow, it may be a good time to think about doing this, but the transformation of the user interface code will have to be done by someone in their spare time. Are you familiar with any automated tools for creating and maintaining internationalization bundles ? 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 ap3 at sanger.ac.uk Fri Jul 11 11:13:43 2008 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Fri Jul 11 11:13:54 2008 Subject: [Jalview-discuss] Jalview and i18n In-Reply-To: <487478DF.2010808@compbio.dundee.ac.uk> References: <48733289.30000@compbio.dundee.ac.uk> <00A50D9B-B1A3-495B-A739-CC783CF6D006@ac-nice.fr> <487478DF.2010808@compbio.dundee.ac.uk> Message-ID: <2129CC65-9FD3-4A87-9803-BC9C907F50AD@sanger.ac.uk> Hi Jim, A strategy for adding internationalization could be: In Eclipse you can do "Externalize Strings" which can move String declarations into external properties files. These properties files can easily get translated into different languages (they are text only) and they then carry different file names depending on the language support they provide. This can then be used by Java automatically to switch to the correct translation based on the Locale. http://java.sun.com/docs/books/tutorial/i18n/index.html An example in terms of source code, see below. Hope that helps, Cheers Andreas rather than doing JButton button = new JButton("press here"); you would say JButton button = new JButton (ResourceManager.getString ("org.jalview.button")); where the resourcemanager looks like below: import java.util.ResourceBundle; import java.util.MissingResourceException; import java.util.logging.Logger; public class ResourceManager { private static final String BUNDLE_NAME = "jalview"; private static final ResourceBundle RESOURCE_BUNDLE = ResourceBundle.getBundle(BUNDLE_NAME); public static Logger logger = Logger.getLogger (JalviewDefaults.LOGGER); private ResourceManager() { } public static String getString(String key) { try { return RESOURCE_BUNDLE.getString(key); } catch (MissingResourceException e) { logger.config(e.getMessage()); return '!' + key + '!'; } } } and the jalview.properties file contains org.jalview.button = press here and since I am a german speaker here goes the german translation: jalview_de_DE.properties has the content org.jalview.button = hier dr?cken (eventually the ResourceManager needs a few more lines of code to check if the default locale is available as a translation and if not, fall back to en_GB, I could help out with that, if needed...) Cheers, Andreas On 9 Jul 2008, at 09:37, James Procter wrote: > Hello Paul. > > Paul Pillot wrote: >> I am a biology teacher for secondary education in France and would >> like >> to use Jalview with my students. I was wondering if there is any plan >> for internationalization or if I should look into creating another >> Jalview version through a translation of the code ? > It would be best if the Jalview source did not fork into > internationalized and 'en-only' versions. However, we have not > explicitly planned for internationalization but it has been requested > quite frequently, and would obviously be of great benefit! > > Now that Jalview development is slow, it may be a good time to think > about doing this, but the transformation of the user interface code > will > have to be done by someone in their spare time. Are you familiar with > any automated tools for creating and maintaining internationalization > bundles ? > > 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. > _______________________________________________ > Jalview-discuss mailing list > Jalview-discuss@jalview.org > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From jimp at compbio.dundee.ac.uk Fri Jul 11 11:39:10 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Fri Jul 11 11:39:27 2008 Subject: [Jalview-discuss] Jalview and i18n In-Reply-To: <2129CC65-9FD3-4A87-9803-BC9C907F50AD@sanger.ac.uk> References: <48733289.30000@compbio.dundee.ac.uk> <00A50D9B-B1A3-495B-A739-CC783CF6D006@ac-nice.fr> <487478DF.2010808@compbio.dundee.ac.uk> <2129CC65-9FD3-4A87-9803-BC9C907F50AD@sanger.ac.uk> Message-ID: <4877384E.8030805@compbio.dundee.ac.uk> G'day Andreas! Andreas Prlic wrote: > A strategy for adding internationalization could be: > > In Eclipse you can do "Externalize Strings" which can move String > declarations into external properties files. These properties files can > easily get translated into different languages (they are text only) and > they then carry different file names depending on the language support > they provide. This can then be used by Java automatically to switch to > the correct translation based on the Locale. > > http://java.sun.com/docs/books/tutorial/i18n/index.html > > An example in terms of source code, see below. Thanks very much! I was, indeed, planning to have a go at the source with the Externalize strings function. It looks like the soruce code transformation is very controllable, and relatively painless, but I still need to work out the fine details of how the different Locale bundles will be managed after the transformation is made (one issue is source code documentation, of course!). My cautiousness is because I've had experience in the past with programs where the internationalization as gotten out of sync with the software UI... which can lead to great user confusion ! Any help or advice on how to manage this would be *greatly* appreciated. Paul and I, and Geoff and I, have been discussing this off-list, and I think it shouldn't take too long to transform Jalview. I'll post news on the list concerning how we get on with this. I'll set up a a prototype internationalized bundle for the applet and the application, and Paul has already volunteered (thanks ;) to help with a first translation of the UI messages into French. However, no guarantees on how long it'll be before we've done this! 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 Thu Jul 17 10:59:13 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Thu Jul 17 10:59:23 2008 Subject: [Jalview-discuss] Re: installation problems In-Reply-To: <1216286375.21474.26.camel@adenine> References: <1216226046.21474.6.camel@adenine> <487E2A25.4080207@compbio.dundee.ac.uk> <1216286375.21474.26.camel@adenine> Message-ID: <487F17F1.60306@compbio.dundee.ac.uk> Hi Daniel. This is cc'ed to the jalview-discuss list, just in case anyone out there has had/dealt with this problem already. Jim edited what Daniel Rigden wrote: > I've just got a new machine, running (64 bit) Ubuntu 8.04, and I'd > like to get Jalview working on it. Unfortunately, both > [InstallAnywhere and webstart] methods fail for me. > > I first tried install anywhere, including jre, but I get a series > of errors like 'Locking assertion failure'. > > I got this when installing for the first time, and when subsequently > trying to run it. > > On Web Start off the webpage, the Exception text goes like this > > JNLPException[category: Download Error : Exception: > java.net.UnknownHostException: www.jalview.org : LaunchDesc: null ] > at > com.sun.javaws.cache.DownloadProtocol.doDownload(DownloadProtocol.java:611) > at > com.sun.javaws.cache.DownloadProtocol.getDownloadSize(DownloadProtocol.java:808) > at > com.sun.javaws.LaunchDownload.downloadJarFiles(LaunchDownload.java:674) > at > com.sun.javaws.LaunchDownload.downloadEagerorAll(LaunchDownload.java:638) > at com.sun.javaws.Launcher.downloadResources(Launcher.java:969) > at com.sun.javaws.Launcher.handleApplicationDesc(Launcher.java:335) > at com.sun.javaws.Launcher.handleLaunchFile(Launcher.java:217) > at com.sun.javaws.Launcher.run(Launcher.java:164) > at java.lang.Thread.run(Thread.java:595) um. clear as mud. looks like www.jalview.org is not resolving for the javaws program, which is pretty serious. I've seen this kind of thing when the JNLP is broken - but both jalview.org and the ws-dev1 JNLP files work fine on Sun java 4,5,and 6 javaws implementations. > I'm perfectly happy to use the command line. I installed openjdk and > pointed JAVA_HOME to /usr/lib/jvm/ [don't know if that's right] > > Then I get > > daniel@adenine:~/progs/jalview_cl$ java -Djava.ext.dirs=. > jalview.bin.Jalview > Java version: 1.6.0 > amd64 Linux 2.6.24-19-generic > Jalview Version: Automated Build > Exception in thread "Thread-0" java.lang.NullPointerException > at java.util.Hashtable.put(Hashtable.java:411) > at java.util.Properties.setProperty(Properties.java:160) > at java.lang.System.setProperty(System.java:748) > at jalview.bin.Cache$1VersionChecker.run(Cache.java:269) > Exception in thread "main" java.awt.AWTError: Assistive Technology not > found: org.GNOME.Accessibility.JavaBridge > at java.awt.Toolkit.loadAssistiveTechnologies(Toolkit.java:788) > at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:874) > at > javax.swing.UIManager.getSystemLookAndFeelClassName(UIManager.java:617) > at jalview.bin.Jalview.main(Jalview.java:122) yuk. That looks like an issue with the installation of openJDK. I have to admit, we have not had much luck at all with *any* non sun JVMs - did you have a go with the sun 1.(4,5,6) JRE - particularly - try the 32bit version ? (googling the java.awt.AWTError yielded a page which suggests this isn't an openJDK issue though, so.. no idea - herer really). > I appear not to have BERYL installed (though it looks quite cool) There are some more explicit guidlines which are Compiz/Beryl related... but it might be something that helps this issue too (the issues are all LookAndFeel related.. so...). You could give them a go and see what happens - : http://66.102.9.104/search?q=cache:ED_njtYjQQcJ:dmartin.org/weblog/how-to-get-java-swing-apps-working-under-beryl-or-compiz-including-java-web-start+how-to-get-java-swing-apps-working-under-beryl-or-compiz-including-java-web-start&hl=en&client=firefox-a&gl=uk&strip=1 (this is a google-cached version of a blog entry that isn't accessible any more...) I'll have an ask around to see if anyone else in the lab has a recent ubuntu install. There may be some workarounds I can introduce into jalview to get it going on your system... but until then, the floor is open to you all at jalview-discuss ! Jim From jimp at compbio.dundee.ac.uk Thu Jul 17 13:51:14 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Thu Jul 17 13:51:31 2008 Subject: [Jalview-discuss] Re: installation problems In-Reply-To: <1216291337.21474.43.camel@adenine> References: <1216226046.21474.6.camel@adenine> <487E2A25.4080207@compbio.dundee.ac.uk> <1216286375.21474.26.camel@adenine> <487F17F1.60306@compbio.dundee.ac.uk> <1216291337.21474.43.camel@adenine> Message-ID: <487F4042.6020708@compbio.dundee.ac.uk> Daniel Rigden wrote: > Hi James > > I appear to have a solution that works, although some errors still pop > up. I removed the openjdk and instead installed sun's 1.6 jre. Then I > set JAVA_HOME and did your > java -Djava.ext.dirs=. jalview.bin.Jalview > > The first time I did this, although Jalview window opened everything was > a mess and non-functional. There were huge numbers of errors. The > *second* time I get something that appears to work perfectly. ok - odd - normally errors like this are reproducible - maybe something got set up after the first run. However, > I do get this upon starting up > > daniel@adenine:~/progs/jalview_cl$ java -Djava.ext.dirs=. > jalview.bin.Jalview > Java version: 1.6.0_06 > amd64 Linux 2.6.24-19-generic > Jalview Version: Automated Build > Exception in thread "Thread-0" java.lang.NullPointerException > at java.util.Hashtable.put(Hashtable.java:394) > at java.util.Properties.setProperty(Properties.java:143) > at java.lang.System.setProperty(System.java:731) > at jalview.bin.Cache$1VersionChecker.run(Cache.java:269) this exception isn't serious. its a minor bug in the jalview version check code that is just about to be fixed. > Later, I get this > > Exception in thread "AWT-EventQueue-0" > java.lang.ArrayIndexOutOfBoundsException: No such child: 7 > at java.awt.Container.getComponent(Container.java:281) > at javax.swing.JComponent.rectangleIsObscured(JComponent.java:4337) > at javax.swing.JComponent.paint(JComponent.java:1025) > at javax.swing.JLayeredPane.paint(JLayeredPane.java:564) > at javax.swing.JComponent.paintToOffscreen(JComponent.java:5122) > at > javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:285) > at javax.swing.RepaintManager.paint(RepaintManager.java:1128) > at javax.swing.JComponent._paintImmediately(JComponent.java:5070) > at javax.swing.JComponent.paintImmediately(JComponent.java:4880) > at > javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:723) > at > javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:679) > at > javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:659) > at javax.swing.SystemEventQueueUtilities > $ComponentWorkRequest.run(SystemEventQueueUtilities.java:128) > at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) > at java.awt.EventQueue.dispatchEvent(EventQueue.java:597) > at > java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:273) > at > java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:183) > at > java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:173) > at > java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:164) > at java.awt.Container$2.run(Container.java:2701) > at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) > at java.awt.EventQueue.dispatchEvent(EventQueue.java:597) > at > java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:273) > at > java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:183) > at > java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:173) > at > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:168) > at > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:160) > at java.awt.EventDispatchThread.run(EventDispatchThread.java:121) again - a non-serious exception raised by the windowing system .. one day, it may be fixed (if we can work out how :). > but things seem to carry on working. Are these errors likely to a > problem later? nope. > Hopefully a much simpler question... What alias would I use to set up a > jalview command to run from anywhere in the file hierarchy, not just > where jalview was installed? basically, a shell script like this would do it : #!/bin/bash JALVIEW_HOME=/path to jalview lib dir JAVA_HOME=/path to java jre dir $JAVA_HOME/bin/java -Djava.ext.dirs=$JALVIEW_HOME jalview.bin.Jalview $@ save it somewhere on your $PATH and make sure its executable, and all should work. I really think that you should be able to get the webstart version working now you have the sun jvm installed. You'll need to make sure that the javaws executable from the sun JRE is being used to start jalview - you should be able to find it under the bin directory of the JRE (/bin/javaws), but it seems to wander around between different JVM installations. if you could find a javaws executable under that path then you should be able to do something like: /bin/javaws http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/latest/webstart/jalview.jnlp to start up Jalview via webstart. Obviously, you'd also need to fix your web browser to launch the correct javaws executable, as well. good to hear things are working for you now! Jim From jimp at compbio.dundee.ac.uk Thu Jul 17 15:52:21 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Thu Jul 17 15:52:38 2008 Subject: [Jalview-discuss] Re: installation problems In-Reply-To: <1216304878.21474.59.camel@adenine> References: <1216226046.21474.6.camel@adenine> <487E2A25.4080207@compbio.dundee.ac.uk> <1216286375.21474.26.camel@adenine> <487F17F1.60306@compbio.dundee.ac.uk> <1216291337.21474.43.camel@adenine> <487F4042.6020708@compbio.dundee.ac.uk> <1216304878.21474.59.camel@adenine> Message-ID: <487F5CA5.4080508@compbio.dundee.ac.uk> Hi Dan. Thanks for getting back to me. Daniel Rigden wrote: > In fact the Webstart still doesn't work. I get this exception > > com.sun.deploy.net.FailedDownloadException: Unable to load resource: > http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/latest/webstart/jalview.jar > at com.sun.deploy.net.DownloadEngine.actionDownload(Unknown Source) > at com.sun.deploy.net.DownloadEngine.getCacheEntry(Unknown Source) > at com.sun.deploy.net.DownloadEngine.getResourceCacheEntry(Unknown > Source) > at com.sun.deploy.net.DownloadEngine.getResourceCacheEntry(Unknown > Source) > at com.sun.deploy.net.DownloadEngine.getResource(Unknown Source) > at com.sun.javaws.LaunchDownload.downloadJarFiles(Unknown Source) > at com.sun.javaws.LaunchDownload.downloadEagerorAll(Unknown Source) > at com.sun.javaws.Launcher.downloadResources(Unknown Source) > at com.sun.javaws.Launcher.prepareLaunchFile(Unknown Source) > at com.sun.javaws.Launcher.prepareToLaunch(Unknown Source) > at com.sun.javaws.Launcher.launch(Unknown Source) > at com.sun.javaws.Main.launchApp(Unknown Source) > at com.sun.javaws.Main.continueInSecureThread(Unknown Source) > at com.sun.javaws.Main$1.run(Unknown Source) > at java.lang.Thread.run(Unknown Source) > > That's directing the browser to open it with javaws from > jre-6u7-linux-i586.bin. ... sigh. ok. Notwithstanding any Proxy issues, it does look like something is very broken. if the shell wrapper works then I'd go with that for the moment - there still seems to be some installation issues with the JVM. We do have some x86_64 machines that can be used to test InstallAnywhere, and I'll post something to you (and the list) sometime when I get to the bottom of this. happy jalviewing (hopefully...) .. Jim. From avilella at gmail.com Thu Jul 17 16:48:44 2008 From: avilella at gmail.com (Albert Vilella) Date: Thu Jul 17 16:49:14 2008 Subject: [Jalview-discuss] rendering problems Message-ID: <358f4d650807170848p3608ad0biecd34884903f0568@mail.gmail.com> Hi, I've installed the latest Jalview for linux, and I seem to have rendering problems on it. It looks like the windows are not refreshing the image, and it's only when I move the mouse over them or shake the windows a bit that the content of the window is partially displayed. Here are three examples: http://www.ebi.ac.uk/~avilella/jalview1.png # The menu shows up only when I resize the window http://www.ebi.ac.uk/~avilella/jalview2.png # The window frame for the tree doesn't show http://www.ebi.ac.uk/~avilella/jalview3.png # Moving the threshold on the tree makes the aligment look garbled Any ideas? Cheers, Albert. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.jalview.org/pipermail/jalview-discuss/attachments/20080717/ba60243a/attachment.htm From jimp at compbio.dundee.ac.uk Thu Jul 17 17:06:22 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Thu Jul 17 17:06:36 2008 Subject: [Jalview-discuss] rendering problems In-Reply-To: <358f4d650807170848p3608ad0biecd34884903f0568@mail.gmail.com> References: <358f4d650807170848p3608ad0biecd34884903f0568@mail.gmail.com> Message-ID: <487F6DFE.3040101@compbio.dundee.ac.uk> Hello Albert. Albert Vilella wrote: > I've installed the latest Jalview for linux, and I seem to have > rendering problems on it. It looks like the windows > are not refreshing the image, and it's only when I move the mouse over > them or shake the windows a bit that the content of the window is > partially displayed. > > Here are three examples: > > http://www.ebi.ac.uk/~avilella/jalview1.png # The menu shows up only > when I resize the window > http://www.ebi.ac.uk/~avilella/jalview2.png # The window frame for the > tree doesn't show > http://www.ebi.ac.uk/~avilella/jalview3.png # Moving the threshold on > the tree makes the aligment look garbled > > Any ideas? Just of the top of my head, are you using Compiz or Beryl as a window manager ? There are (still) some issues with Swing applications using these managers. http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6429775 I've noticed some occasional redraw issues with older linuxen - but nothing like what you've shown in those snapshots. 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 Tue Jul 29 17:44:35 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue Jul 29 17:45:13 2008 Subject: [Jalview-discuss] Re: Jalview Sequence Fetcher has stopped working In-Reply-To: <1B314609ED89A2449037E67690426B2316EAAD@HERMES1.ds.leeds.ac.uk> References: <1B314609ED89A2449037E67690426B2316EAAC@HERMES1.ds.leeds.ac.uk> <488DAD83.2070409@compbio.dundee.ac.uk> <1B314609ED89A2449037E67690426B2316EAAD@HERMES1.ds.leeds.ac.uk> Message-ID: <488F48F3.8090106@compbio.dundee.ac.uk> Hi All. I've just verified that the Uniprot XML schema has just been updated, and the Jalview Sequence Fetcher is now playing catchup - that is - you will currently not be able to retrieve sequences from the EBI using the 'fetch Sequences' dialog in the jalview application. > Daryl Tacon wrote: >> Hi, I have had Jalview running successfully on my PC. Unfortunately, the fetch sequences function has stopped working Thanks for alerting me to this Daryl - watch this list for news of when the development version : http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/release/webstart/jalview.jnlp is updated. 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 Thu Jul 31 11:29:22 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Thu Jul 31 11:29:41 2008 Subject: [Jalview-discuss] Re: Jalview Sequence Fetcher has stopped working In-Reply-To: <488F48F3.8090106@compbio.dundee.ac.uk> References: <1B314609ED89A2449037E67690426B2316EAAC@HERMES1.ds.leeds.ac.uk> <488DAD83.2070409@compbio.dundee.ac.uk> <1B314609ED89A2449037E67690426B2316EAAD@HERMES1.ds.leeds.ac.uk> <488F48F3.8090106@compbio.dundee.ac.uk> Message-ID: <48919402.2050906@compbio.dundee.ac.uk> I just checked in the fix to the Uniprot XML parser in the development version - it appears to work but do let me know if things are behaving differently: http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/release/webstart/jalview.jnlp Jim ps. another fix may come today for the PFAM fetcher - which also appears to be out of sync with PFAM's retrieval URLs.