User-created annotation warning icons - implement more and improve UI

[strumpfe]

One of the great features of WebApollo is the mark up of potential errors in the user-created annotations on the fly allowing users to correct them there and then. My understanding is this is currently limited to non-canonical splice sites but I'd like to argue for expanding the list of error checks and a simple improvement of the UI.

// Adding lack of stop codon as a warning icon. WebApollo aggressively re-assigns initiation methionine residues based on the potential/maximal ORF prediction - that is if I drag extend a 5' exon the CDS will be recalculated to the first ATG. Its actually quite difficult to make a prediction with no ATG without explicitly invoking the 'Set Translation Start' option. It is however easy to create a prediction with no Stop codon. Personally I like to include the stop codon as part of the mature mRNA even when there is no 3' UTR predicted. I'm aware there is a difference of opinion here but being aware of a potential partial prediction is important.

Hence, I'd propose a 'No stop codon asserted' warning icon to indicate when partial predictions are likely. In my world this means that in the absence of a 3' UTR the final 3 bp of the mRNA should be a stop codon. In a FlyBase/Chado world and in the absence of a 3' UTR the 3 bp immediately 3' of the mRNA should be a stop codon triplet. I'm happy to go into further details here if this is unclear or you want to discuss the merits of including or excluding stop codons in predictions.

// Improved UI of warning icons When you do get a waning icon on a user-created prediction there are two improvements that could be implemented.

Firstly, have a popup bubble which defines the reason this warning has been invoked e.g. Non-canonical splice site XX. This would make it easier to distinguish between the uncommon but valid non-canonical GC splice donor with outright bad splice donor/acceptors.

Secondly, if a user clicked on the icon jbrowse should zoom to base level so that the region can be investigated. Currently one has to select a small region or hope to align the mouse close enough to the correct coordinates and right-click -> Zoom to base level such that you end up at the right place. Making the warning clickable should make checking/correcting of the errors a more efficient task

[nathandunn]

There are a lot of great ideas in here. I know that @mpoelchau (sp?) @childers had proposed similar ideas (better error checking), but more in a report phase.

[strumpfe]

Reporting of errors for the altruistic curator to fix is good but highlighting them at the point of generation encourages the original user to correct them at source. This is a prime exemplar of "prevention is better than cure".

[nathandunn]

:+1: