biodiverse
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20 hours ago •
shawnlaffan
shawnlaffan
Site Pair Sampler - clean up the internals, refactor components
The Site Pair Sampler script works well, but needs a clean up of the internals
as well as a refactoring to make it possible to run from a single script using
a parameters file, as opposed to one script for each instance.
The package namespace should probably be shifted over to Biodiverse at some
point, e.g. Biodiverse::SitePairSampler.
Original issue reported on code.google.com by shawnlaffan on 26 Nov 2012 at 4:16
This issue was updated by revision r1392.
Shift the distance table calculation to its own package. It doesn't use
BdPD::GDM_Input objects.
Reformat the code to be closer to the rest of the Biodiverse project.
Move subs new, initialise and set_param near to the top. They will be at the
top when generate_distance_tablexx is deleted.
Original comment by shawnlaffan on 26 Nov 2012 at 4:20
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This issue was updated by revision 1399
Add support for a file of arguments that is not a perl data structure.
Tidy up some of the code formatting (need to run perltidy on it)
Original comment by shawnlaffan on 5 Dec 2012 at 2:44
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This issue was updated by revision r1400.
Add example arguments file (with temp name).
Skip empty lines (those without a keyword after stripping comments and
whitespace etc) when parsing the args file.
Original comment by shawnlaffan on 5 Dec 2012 at 2:45
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This issue was updated by revision r1405.
Ugly hack to make the code find the biodiverse libs
Original comment by shawnlaffan on 11 Dec 2012 at 11:26
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This issue was updated by revision r1406.
Handle tree import when no remap file is specified.
Original comment by shawnlaffan on 11 Dec 2012 at 11:33
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The new version is working with a full set of species and phylo parameters.
Haven't checked the 'no remap file is specified' option yet.
Original comment by danielrosauer on 13 Dec 2012 at 10:51
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