Optimize multi-tree comparisons#59

Draft

ms609 wants to merge 83 commits intomainfrom

Commits on Jul 19, 2021

pre-increment
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Header guards
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alpha
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start work on cpp_all_pairs_mci()
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Constructing tournament tree
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Play first games
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Commits on Jul 20, 2021

Test for equality at end
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File reorganization
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.h → .hpp
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Initialize SplitRoster()
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int32s
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Log splits
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Tournament implementation
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Save winners & losers
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Simplify
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.hpp
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Declarations
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vector of arrays
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in_split is int16
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types
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index format
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hpp
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std::vector<SplitList> splits
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hpp
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Correct assertions
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emplace_back takes params only
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mvoe up
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begin cpp_all_pairs_mci
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Commits on Jul 21, 2021

Framework for self-comparison
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Draft of score_pairs()
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Draft ready to debug?
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Update tree_distances.cpp
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Merge branch 'master' into optim
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return
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parent/child offset
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Debug
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new_split
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SplitList(RawMatrix x, int16 n_tip);
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//
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#define
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leaves
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, n_tips
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na/nA switch
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li
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sp_i/j
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max-/
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max lookip
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n_trees - 1
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Swap in_split
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nA, na
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n_tips
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Working for 9 leaves
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//
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Commits on Jul 22, 2021

* Use MACROS for SplitList(x)
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i = winner + tournament_games
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Update SplitRoster.cpp
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pow → <<
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Full bin
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Update SplitList.cpp
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index for 0!
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Debugging comments
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INBIN not INSUBBIN
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assert(fuzzy_match < lap_dim);
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Merge branch 'master' into optim
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Merge branch 'master' into optim
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Update SplitList.cpp
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Improve comment
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ws
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ai:→ roster_len
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Drop TR1 reference
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.hpp→.h
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.hpp→.h
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.hpp→.h
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.hpp→.h
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Don't calculate self-similarity
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spell 'dist'
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// entry++
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Populate spare j-splits
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spacing
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don't invert
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consts → #defines
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use memory once
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ws
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