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Don't perform layout on connected components containing just one node #252

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fedarko opened this issue Aug 2, 2017 · 2 comments
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Don't perform layout on connected components containing just one node #252

fedarko opened this issue Aug 2, 2017 · 2 comments
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codeissue collateoptimization

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fedarko commented Aug 2, 2017 •
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The repeated costs of running sfdp (in SPQR mode) and dot (in standard mode) on cc's of single nodes aren't that bad when the number of those components is less than around 1000, but this quickly gets out of hand when there are literally tens of thousands of those components (for the one graph I'm working with now there's over 100k "single-node" components).

Solution: for a component containing a single node of width w inches and h inches, with no edges and with no node groups, just set the bounding box of the resulting connected components (in SPQR and standard mode) to (w + some padding, h + some padding). Look at some current ways Graphviz lays this stuff out for guidance.

This has the potential to save a lot of time (by preventing lots of repeated calls to pygraphviz).
@fedarko fedarko self-assigned this Aug 2, 2017
fedarko added a commit that referenced this issue Aug 2, 2017
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Add comments to collate.py re: #165, #252
36e0518
fedarko added a commit that referenced this issue Aug 5, 2017
@fedarko
Compute SPQR unc. node ct & show in layout msgs
3c54ece 
Closes #197! It should be a lot easier to get a handle on the
progress of laying out SPQR-mode connected components now.

This will make working on #252 a lot easier.
fedarko added a commit that referenced this issue Aug 5, 2017
@fedarko
Add detection code for 1-node ccs in stdmode #252
28e4933 
Still need to actually add layout circumvention. will take care of
that later tonight.
@fedarko fedarko mentioned this issue Aug 7, 2017
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fedarko commented Aug 7, 2017

got algorithm mostly figured out by this point; will implement tomorrow

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fedarko commented Aug 9, 2017

This issue was moved to marbl/MetagenomeScope#1

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