Allow extinct species without extinction dates

[hyanwong]

At the moment, we identify extinct species by the fact that their entry in the ordered_leaves table has a positive floating point number (in millions of years) in the extinction_date column (there are only 3 such leaves at the moment). Species that are not extinct have NULL in that column.

The new version of the OpenTree will include extinct taxa, but will not contain their extinction dates. We need a way to mark taxa as extinct but with no date. We could possibly do this by using a placeholder value (annoyingly, mySQL doesn't allow NaN, +inf, or -inf, so a suggested placeholder would either be a number larger than 5000 (as they cannot be older than 5000 million years ago, the age of the earth), or possibly a negative number (e.g. -1e4)

[hyanwong]

My inclination is to use -1e4 and check for branch lengths < -5e3. It used to be the case that I used negative branch lengths to indicate uncertain taxon placement (see tree in OZprivate/data/OZTreeBuild/AllLife/BespokeTree/include_files/Apusozoa_plus.PHY ), but I'm not sure what the code does with negative branch lengths now.

[hyanwong]

It looks like these are simply ignored, and the length set to 0 (indicating a polytomy) -

OZtree/OZprivate/ServerScripts/TaxonMappingAndPopularity/dendropy_extras.py

Line 106 in 1cf5f6c

l=0 if l<0 else l

[hyanwong]

Started coding on the Extinct-taxa branch