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-generic DEBUG - find: resourceName='commons-logging.properties' DEBUG - getNextResources: search using ClassLoader 'sun.misc.Launcher$AppClassLoader@4e25154f' DEBUG - Could not find resource: commons-logging.properties DEBUG - find: resourceName='org/apache/commons/logging/commons-logging.properties' DEBUG - getNextResources: search using ClassLoader 'sun.misc.Launcher$AppClassLoader@4e25154f' DEBUG - Could not find resource: org/apache/commons/logging/commons-logging.properties DEBUG - find: serviceName = 'META-INF/services/org.apache.commons.logging.LogFactory' DEBUG - find: resourceName='META-INF/services/org.apache.commons.logging.LogFactory' DEBUG - getNextResources: search using ClassLoader 'sun.misc.Launcher$AppClassLoader@4e25154f' DEBUG - Could not find resource: META-INF/services/org.apache.commons.logging.LogFactory DEBUG - find: className='org.apache.commons.logging.impl.LogFactoryImpl' DEBUG - getNextClass: next URL='jar:file:/usr/share/java/commons-logging.jar!/org/apache/commons/logging/impl/LogFactoryImpl.class' DEBUG - loadClass: Loading class 'org.apache.commons.logging.impl.LogFactoryImpl' with sun.misc.Launcher$AppClassLoader@4e25154f 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 3:31:26 PM INFO - Saved last read date as May 20, 2015 3:31:26 PM INFO - Saved last read date as May 20, 2015 3:31:26 PM Building ws menu again Thread[Thread-17,6,main] Exception for url:http://www.dasregistry.org/das1/sources/ java.io.FileNotFoundException: http://www.dasregistry.org/das1/sources/ at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1835) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1440) at org.biojava.dasobert.das2.io.DasSourceReaderImpl.open(DasSourceReaderImpl.java:53) at org.biojava.dasobert.das2.io.DasSourceReaderImpl.readDasSource(DasSourceReaderImpl.java:65) at jalview.ws.DasSequenceFeatureFetcher.getDASSources(DasSequenceFeatureFetcher.java:865) at jalview.ws.DasSequenceFeatureFetcher.getDASSources(DasSequenceFeatureFetcher.java:848) at jalview.ws.SequenceFetcher.registerDasSequenceSources(SequenceFetcher.java:320) at jalview.ws.SequenceFetcher.<init>(SequenceFetcher.java:64) at jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(SequenceFetcher.java:118) at jalview.gui.AlignFrame$17.run(AlignFrame.java:4852) at java.lang.Thread.run(Thread.java:745) ________________________________________ From: Jim Procter [[email protected]] on behalf of Jim Procter [[email protected]] Sent: 25 May 2015 15:47 To: Ganesh Phad; [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 !). Jim _______________________________________________ Jalview-discuss mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
