Mungo - do you feel the need to patch 2.11.1 to fix up its behaviour ?
(ps - cced jalview-dev…).
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) J.Procter@dundee.ac.uk
Sent: 14 November 2019 13:21
To: Mungo Carstairs (Staff) g.m.carstairs@dundee.ac.uk; Mateusz Warowny (Student) m.m.warowny@dundee.ac.uk
Subject: Re: Matching protein / nucleotide services to alignments in JalviewActually 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.
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
Mungo Carstairs
Jalview Computational ScientistThe Barton Group
Division of Computational BiologySchool of Life Sciences
University of Dundee, Dundee, Scotland, UK
www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk
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On 14/11/2019 13:24, Mateusz Warowny (Staff) wrote:
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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)