search

diegozea / MIToS.jl

A Julia package to analyze protein sequences, structures, and evolutionary information
https://diegozea.github.io/MIToS.jl/stable/
Other
75 stars 18 forks source link

`count!` performance #30

Closed diegozea closed 7 years ago

diegozea commented 8 years ago

count!, when GAPs aren't used in the ResidueContingencyTables, tests if each residue is a gap in order to avoid indexing outside the bonds. This is expensive and prevent us to use @simd. ResidueContingencyTables should have always 22x22 values, even if only 20 will be used.

diegozea commented 7 years ago

MIToS 2.0 uses ContingencyTable. That object stores a temporal array. This array is 22x22 in a bidimensional case and it's used to avoid the use of if when the table is filled. It's 22 to avoid checking for GAP or X.