Hi Jim, I used a installer file (with java VM) available for linux platform from this link - http://www.jalview.org/Web_Installers/install.htm and then I think I had to download/install jdk, don't remember exactly, anyway, a new version you sent is working, I could copy the consensus sequence when I right click near the consensus name and not on the histogram so that's good. Thanks for a quick replies and help!
Best, G From: Jim Procter [[email protected]] on behalf of [email protected] [[email protected]] Sent: 25 May 2015 21:45 To: [email protected]; Ganesh Phad Subject: RE: [Jalview-discuss] Consensus sequence extraction on ubuntu How did you install Jalview ? It looks like source build but no build date has been given. Could you try the version at http://www.jalview.org/builds/release/webstart/jalview_2G.jnlp Jim. Sent from my android device. -----Original Message----- From: Ganesh Phad <[email protected]> To: Jim Procter <[email protected]>, "[email protected]" <[email protected]> Sent: Mon, 25 May 2015 18:02 Subject: RE: [Jalview-discuss] Consensus sequence extraction on ubuntu Hi Jim, Thanks, I tried but nothing happens when I right click on the histogram under the alignment, below is the java console output, please let me know what you think. Thanks, Ganesh Jalview Desktop Test Build Date: unknown Java version: 1.8.0_45 amd64 Linux 3.13.0-52<tel:313052>-generic DEBUG - find: resourceName='commons-logging.properties<http://commons-logging.properties>' DEBUG - getNextResources: search using ClassLoader 'sun.misc.Launcher<http://sun.misc.Launcher>$AppClassLoader@4e25154<tel:25154>f' DEBUG - Could not find resource: commons-logging.properties<http://commons-logging.properties> DEBUG - find: resourceName='org/apache/commons/logging/commons-logging.properties<http://commons-logging.properties>' DEBUG - getNextResources: search using ClassLoader 'sun.misc.Launcher<http://sun.misc.Launcher>$AppClassLoader@4e25154<tel:25154>f' DEBUG - Could not find resource: org/apache/commons/logging/commons-logging.properties<http://commons-logging.properties> DEBUG - find: serviceName = 'META-INF/services/org.apache.commons.logging.LogFactory<http://org.apache.commons.logging.LogFactory>' DEBUG - find: resourceName='META-INF/services/org.apache.commons.logging.LogFactory<http://org.apache.commons.logging.LogFactory>' DEBUG - getNextResources: search using ClassLoader 'sun.misc.Launcher<http://sun.misc.Launcher>$AppClassLoader@4e25154<tel:25154>f' DEBUG - Could not find resource: META-INF/services/org.apache.commons.logging.LogFactory<http://org.apache.commons.logging.LogFactory> DEBUG - find: className='org.apache.commons.logging.impl.LogFactoryImpl<http://org.apache.commons.logging.impl.LogFactoryImpl>' DEBUG - getNextClass: next URL='jar:file:/usr/share/java/commons-logging.jar<http://commons-logging.jar>!/org/apache/commons/logging/impl/LogFactoryImpl.class<http://LogFactoryImpl.class>' DEBUG - loadClass: Loading class 'org.apache.commons.logging.impl.LogFactoryImpl<http://org.apache.commons.logging.impl.LogFactoryImpl>' with sun.misc.Launcher<http://sun.misc.Launcher>$AppClassLoader@4e25154<tel:25154>f WARN - Exception when discovering One Way services: WARN - Exception when discovering One Way services: INFO - Not enabling Google Tracking. INFO - Constructing news reader. Discovered service: http://www.compbio.dundee.ac.uk/jabaws MafftWS INFO - Completed construction of reader. Discovered service: http://www.compbio.dundee.ac.uk/jabaws MuscleWS Discovered service: http://www.compbio.dundee.ac.uk/jabaws ClustalWS Discovered service: http://www.compbio.dundee.ac.uk/jabaws TcoffeeWS Discovered service: http://www.compbio.dundee.ac.uk/jabaws ProbconsWS INFO - Saved last read date as May 20, 2015 3<tel:20153>:31:26 PM INFO - Saved last read date as May 20, 2015 3<tel:20153>:31:26 PM INFO - Saved last read date as May 20, 2015 3<tel:20153>:31:26 PM Building ws menu again Thread[Thread-17,6,main] Exception for url:http://www.dasregistry.org/das1/sources/ java.io.FileNotFoundException<http://java.io.FileNotFoundException>: http://www.dasregistry.org/das1/sources/ at sun.net.www.protocol.http.HttpURLConnection<http://sun.net.www.protocol.http.HttpURLConnection>.getInputStream0(HttpURLConnection.java:1835<http://HttpURLConnection.java:1835>) at sun.net.www.protocol.http.HttpURLConnection.getInputStream<http://sun.net.www.protocol.http.HttpURLConnection.getInputStream>(HttpURLConnection.java:1440<http://HttpURLConnection.java:1440>) at org.biojava.dasobert.das2.io.DasSourceReaderImpl.open<http://org.biojava.dasobert.das2.io.DasSourceReaderImpl.open>(DasSourceReaderImpl.java:53<http://DasSourceReaderImpl.java:53>) at org.biojava.dasobert.das2.io.DasSourceReaderImpl.readDasSource<http://org.biojava.dasobert.das2.io.DasSourceReaderImpl.readDasSource>(DasSourceReaderImpl.java:65<http://DasSourceReaderImpl.java:65>) at jalview.ws.DasSequenceFeatureFetcher.getDASSources<http://jalview.ws.DasSequenceFeatureFetcher.getDASSources>(DasSequenceFeatureFetcher.java:865<http://DasSequenceFeatureFetcher.java:865>) at jalview.ws.DasSequenceFeatureFetcher.getDASSources<http://jalview.ws.DasSequenceFeatureFetcher.getDASSources>(DasSequenceFeatureFetcher.java:848<http://DasSequenceFeatureFetcher.java:848>) at jalview.ws.SequenceFetcher.registerDasSequenceSources<http://jalview.ws.SequenceFetcher.registerDasSequenceSources>(SequenceFetcher.java:320<http://SequenceFetcher.java:320>) at jalview.ws.SequenceFetcher<http://jalview.ws.SequenceFetcher>.<init>(SequenceFetcher.java:64<http://SequenceFetcher.java:64>) at jalview.gui.SequenceFetcher.getSequenceFetcherSingleton<http://jalview.gui.SequenceFetcher.getSequenceFetcherSingleton>(SequenceFetcher.java:118<http://SequenceFetcher.java:118>) at jalview.gui.AlignFrame<http://jalview.gui.AlignFrame>$17.run<http://17.run>(AlignFrame.java:4852<http://AlignFrame.java:4852>) at java.lang.Thread.run<http://java.lang.Thread.run>(Thread.java:745<http://Thread.java:745>) ________________________________________ From: Jim Procter [[email protected]<mailto:[email protected]>] on behalf of Jim Procter [[email protected]<mailto:[email protected]>] Sent: 25 May 2015 15<tel:201515>:47 To: Ganesh Phad; [email protected]<mailto:[email protected]> Subject: Re: [Jalview-discuss] Consensus sequence extraction on ubuntu Hi Ganesh On 25/05/2015 14:40, Ganesh Phad wrote: > I'm using jalview on linux (ubuntu) platform and want to know how to extract > consensus sequence from the alignment (right click and copy from consensus > histogram option doesn't seems to work in the ubuntu) Normally this does work (the option copies the consensus to the clipboard, for pasting into an alignment or another program). Could you open the Jalview Java console (Tools->Show Java Console) and try to select the option again ? Please send me any output and I'll investigate (or you could open a bug at issues.jalview.org<http://issues.jalview.org> !). Jim _______________________________________________ Jalview-discuss mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
