Index and other optimisations #922
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Take advantage of the label hash global precalc, and use hash aliases instead of refs.
Might as well avoid any recursion overheads.
And stop throwing errors when ref is undefined in get_basedata_ref.
This was we avoid cloning basedata refs, analysis args and the like.
No need to find the index names when they are in the base_list_ref already. Also use refaliasing to avoid some derefs and declutter loop variables.
Passing in the base list allows fewer grep comparisons. This makes a large difference when there are many lists with many keys.
Passing in the base list allows fewer grep comparisons. This makes a large difference when there are many lists with many keys.
This allows future optimisations when calculating indices for cluster trees.
This allows several indices to be optimised when calculated for cluster nodes, providing they are done starting from the tips. PE has been optimised in this commit.
Avoids a lot of hash creation and deletion with large datasets.
Speeds up PD calcs for cluster trees.
Use a treenode method that caches, rather than repeatedly calling methods to get the same answer.
It is cleaner to pack the node and child names in their own structure. That also enables later additions without adding yet more top level arguments.
Use direct assignment if starting with empty list.
Avoids a lot of copying.
This can be a _very_ hot loop so even small differences add up.
These are cleared as we go to avoid leakage.
If the second neighbour set is empty then the whole and central variants return the same results. So short circuit in these cases.
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A set of optimisations to several index and related calculations.
Summary of main changes: