Sequence Features refactoring

I’ve pushed features/SequenceFeatureRefactor (forked off develop) to the server.

http://issues.jalview.org/browse/JAL-1665

I’ve tested most of the changes manually as per comments in JIRA.

A few details I’m not sure of:

  • ​desktop PopupMenu how to test add sequence features to Links sub-menu

  • not tested output as JSON as not integrated in this branch

  • not sure how to test StockholmFile.print() - haven’t changed code in here yet

  • not sure how to test Vamsas code, DBRefFetcher.transferReferences , PDBChain.transferRESNUMFeatures (but no changes here, should just be a regression test check)

  • TreePanel.changeNames - looks like an orphaned and possibly broken method?

Mungo

The University of Dundee is a registered Scottish Charity, No: SC015096

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Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
College of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk

OK… could you make some new tasks to create tests for some of below ?

I’ve tested most of the changes manually as per comments in JIRA.

A few details I’m not sure of:

  • ​desktop PopupMenu how to test add sequence features to Links sub-menu

there are test data for that. Create a task for it please ?

  • not tested output as JSON as not integrated in this branch

Tochukwu’s the person here… feel free to create+assign to him.

  • not sure how to test StockholmFile.print() - haven’t changed code in here yet

StockholmFile.print() is tested in StockholmFileTest - which exercises it via a round trip. No ticket needed if that test passes correctly (although it’s not a complex dataset/AlignmentI test).

  • not sure how to test Vamsas code,

I’ll have to deal with that one.

  • DBRefFetcher.transferReferences , PDBChain.transferRESNUMFeatures (but no changes here, should just be a regression test check)

Those could be tested via the appropriate data IO test harnesses (jalview.ws.seqfetcher.DbRefFetcherTest and jalview.io.AnnotatedPDBFileInputTest). Again - create some tasks…

  • TreePanel.changeNames - looks like an orphaned and possibly broken method?

you can see what that does via git-blame (aka Team->show annotations). It is orphaned, but will need to be homed in 2.9.x since it’s a mechanism to modify the label string on a phylogenetic tree according to a sequence feature or accession ID (type or database is specified via className). All it needs is a GUI ! Of course, I implemented it back in 2009 when Jalview didn’t really have a functioning bug database…

Jim

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On 19/02/2015 13:20, Mungo Carstairs (Staff) wrote:

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Division of Computational Biology, College of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
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The University of Dundee is registered Scottish charity: No.SC015096