Faster cluster matrix creation #920
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And optimise. Plus some smaller changes.
Makes a difference for matrices where these are called many times.
And fix an overly zealous change from a recent commit. We need $value in more than one place.
Avoids a lot of calls when building matrices.
In such cases caching becomes beneficial as we are often building a matrix and repeatedly calling subs to get the same answer.
The pairwise abc will make all the other calcs faster. The dispatcher allows centralisation of all the logic controlling which inner sub is used, thus removing a lot of repetition.
This avoids needless calls to calc_abc and thus less processing when building cluster matrices.
No need to calculate calc_abc for the phylo variant. This has the knock-on effect of needing to handle arrays and hashes for the element_list[12] args. The intent is to clean that up as part of issue #919.
shawnlaffan
changed the title
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A set of general optimisations to speed up matrix creation for cluster analyses.
Initially focused on the matrix classes but then extended to the index calculations.