No I don't - if we've lived with it this long, it can wait a tiny bit longer for fixing with Slivka services!
Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> [email protected]<mailto:[email protected]> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 ________________________________ From: James Procter (Staff) <[email protected]> Sent: 14 November 2019 13:26 To: Mateusz Warowny (Staff) <[email protected]>; Mungo Carstairs (Staff) <[email protected]> Cc: Jalview Development List <[email protected]> Subject: Re: Matching protein / nucleotide services to alignments in Jalview Mungo - do you feel the need to patch 2.11.1 to fix up its behaviour ? (ps - cced jalview-dev...). On 14/11/2019 13:24, Mateusz Warowny (Staff) wrote: In Slivka each service has classifiers which helps to identify services and and can be used to determine input and output types: e.g JRonn, Globblot are tagged "Protein sequence analysis", msa e.g. Clustal, t_coffee are tagged "Sequence alignment :: Multiple sequence alignment", aacon has "Sequence alignment analysis :: Sequence alignment analysis (conservation)" tag. ________________________________ From: James Procter (Staff) <[email protected]><mailto:[email protected]> Sent: 14 November 2019 13:21 To: Mungo Carstairs (Staff) <[email protected]><mailto:[email protected]>; Mateusz Warowny (Student) <[email protected]><mailto:[email protected]> Subject: Re: Matching protein / nucleotide services to alignments in Jalview Actually covered by JAL-1172 - but is being addressed in the Slivka revamp of Jalview's services in 2.12. https://issues.jalview.org/browse/JAL-1172 j. On 14/11/2019 13:16, Mungo Carstairs (Staff) wrote: Is there, or could there be, a way to identify services (e.g. JRonn, GlobPlot etc) that are for protein alignments only, so that they could be disabled or hidden as menu options in Jalview (or other client) for a DNA or RNA alignment (and vice versa)? Older versions of Jalview show a warning after requesting the service, e.g. "JRonnWS can only be used for amino acid alignments.". This warning was suppressed (2013 by Dan Barton) when RNAAlifold prediction was added (JAL-1358). Jalview behaviour in 2.11 is mixed (up): * you can request disorder prediction for nucleotide but nothing happens, no error message appears * AbstractJabaCalcWorker.getInputSequences() returns null if nucleotide alignment but peptide service * you can request and get a JPred peptide secondary structure prediction for a nucleotide alignment * AACon service is disabled for nucleotide alignments * RNAAlifold is disabled for protein alignments * you can request a Multi-Harmony analysis for a partitioned nucleotide alignment (but it fails) Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> [email protected]<mailto:[email protected]> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 -- ------------------------------------------------------------------- Dr JB Procter, Jalview Coordinator, The Barton Group Division of Computational Biology, School of Life Sciences University of Dundee, Dundee DD1 5EH, UK. +44 1382 388734 | www.jalview.org<http://www.jalview.org> | www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> -- ------------------------------------------------------------------- Dr JB Procter, Jalview Coordinator, The Barton Group Division of Computational Biology, School of Life Sciences University of Dundee, Dundee DD1 5EH, UK. +44 1382 388734 | www.jalview.org<http://www.jalview.org> | www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> The University of Dundee is a registered Scottish Charity, No: SC015096
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