OK.. could you make some new tasks to create tests for some of below ?
On 19/02/2015 13:20, Mungo Carstairs (Staff) wrote:
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
Mungo
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 <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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