Unable to use edge matching to "set as x' end" about apollo

[nathandunn]

By "does not work" it means it is not avaialble as a selection

https://www.dropbox.com/s/9gnn26v0o62kaoc/Screenshot%202014-11-24%2012.36.44.png?dl=0

[nathandunn]

http://icebox.lbl.gov/WebApolloDemo/jbrowse/?loc=Group1.37%3A155618..156622&tracks=DNA%2CAnnotations%2COfficial%20Gene%20Set%20v3.2%2CNurse%20RNA-Seq%20reads&highlight=

[monicacecilia]

Sometimes "Set as 5' (or 3')" is available, sometimes it is not.

[nathandunn]

Pureley on the client side. This set for example.

https://www.dropbox.com/s/lvtlsinmc9pzavc/Screenshot%202014-11-24%2012.39.16.png?dl=0

[nathandunn]

In AnnotTrack.js . . . need to figure out why these are set one way sometimes and others other times. Same function for all . .

updateSetAsFivePrimeEndMenuItem: function() {
var menuItem = this.getMenuItem("set_as_five_prime_end");
var selectedAnnots = this.selectionManager.getSelection();
var selectedEvidence = this.webapollo.featSelectionManager.getSelection();
if (selectedAnnots.length > 1 || selectedEvidence.length > 1) {
menuItem.set("disabled", true);
return;
}
if (selectedEvidence.length == 0) {
menuItem.set("disabled", true);
return;
}
if (!selectedAnnots[0].feature.parent() || !selectedEvidence[0].feature.parent()) {
menuItem.set("disabled", true);
return;
}
if (selectedAnnots[0].feature.get("strand") != selectedEvidence[0].feature.get("strand")) {
menuItem.set("disabled", true);
return;
}
if (!this.canEdit(selectedAnnots[0].feature)) {
menuItem.set("disabled", true);
return;
}
menuItem.set("disabled", false);
},

[nathandunn]

@monicacecilia So the reason is that the strand of that sequence is the opposite of the annotation (-1 vs 1 in this case) whereas all of the other are the same (both 1).

So there are one of two solutions:
1 - an error in the RNASeq import (shouldn't they all be fixed to be the same strand on import) . .. . do we report this error?
2 - we should be able to handle this case?
3 - strandedness should be apparent from the way its drawn (IMO).

I don't think that there is an error (except in the case of 1) but more of a UI issue. Let me know what you think.

[monicacecilia]

ah, that would do it!
I agree, there is not an error. I won't extend myself here so let's discuss more on the UI in person.
Thanks!