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Add assembly finishing tools to the control panel #72

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fedarko opened this issue Aug 12, 2016 · 3 comments
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Add assembly finishing tools to the control panel #72

fedarko opened this issue Aug 12, 2016 · 3 comments
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fedarko commented Aug 12, 2016

And, presumably, exporting the result to a FASTA file (or modified .db file, maybe?).
@fedarko fedarko self-assigned this Aug 12, 2016
@fedarko fedarko changed the title Facilitate manual edge resolution/etc. Add assembly finishing tools to the control panel Jan 20, 2017
fedarko added a commit that referenced this issue Jan 20, 2017
@fedarko
Add inline selected ele info viewing (close #138)
fc20d4b 
Right now the interface is pretty much the same as the old one --
just in a table on the controls div, instead of in a separate dialog.

Still some work to do on this (#138, then #72), but we're making
good progress with the new UI infrastructure.
fedarko added a commit that referenced this issue Apr 16, 2017
@fedarko
Add assembly finishing start/end buttons (#72)
0e1ff77 
They don't really do anything yet, but I'll add functionality for
them soon.
fedarko added a commit that referenced this issue Apr 16, 2017
@fedarko
Add basic assembly finishing feature (close #74)
e8cd169 
TODOs left for this feature (filing under the purview of #72) --

-Make scaffolds play nice with this (since we set autounselectify
to true while in finishing mode). Maybe have scaffolds just highlight
their nodes a certain color (via style classes or something)?
Basically, I want scaffolds to be viewable during finishing mode.
Right now the problem is that they aren't.

-Add undo/redo buttons (for adding nodes), I guess?

-Optionally (?) enforce that paths can only be constructed from
adjacent nodes (e.g. if a node A is the last node on the path, then
node B can only be added to the path if there exists an edge from
A to B).
This was referenced Apr 16, 2017
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fedarko commented Apr 16, 2017

Yeah. TODOs are given in the commit message for e8cd169, in #180, and in #181. Once those TODOs are taken care of to some extent, I'd say this issue can be closed.

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fedarko commented Apr 16, 2017

Namely, the main things left for this issue in particular are:

  1. Adding undo/redo buttons
  2. Restricting finishing to adjacent nodes

I'd like to get more input on desired features before I implement these in particular. Will update this soon with TODOs.

fedarko added a commit that referenced this issue Apr 17, 2017
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Limit finishing to outgoing nodes (#72)
d465bfc 
can automate some stuff (e.g. auto-proceeding on unambiguous
connections) -- todo, do that.
fedarko added a commit that referenced this issue Apr 20, 2017
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Add TODOs re: #72
02c7e69
fedarko added a commit that referenced this issue Apr 24, 2017
@fedarko
Fix error in starting finishing with a "leaf" #72
335c88b
fedarko added a commit that referenced this issue May 2, 2017
@fedarko
Add partial auto-finishing features (#72)
6603501 
Still needs to account for unambiguous edges from first finishing
node, and could stand to be more efficient.

Other features to add -- coloring the "dock" node that is the source
of the potential nodes to add differently, and making the code a lot
more readable via reusing stuff.
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fedarko commented Aug 9, 2017

This issue was moved to marbl/MetagenomeScope#11

@fedarko fedarko mentioned this issue Aug 9, 2017
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@fedarko fedarko closed this as completed Aug 9, 2017
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