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properly integrate gquad #61

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5 tasks
sjanssen2 opened this issue Mar 1, 2023 · 0 comments
Open
5 tasks

properly integrate gquad #61

sjanssen2 opened this issue Mar 1, 2023 · 0 comments

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@sjanssen2
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sjanssen2 commented Mar 1, 2023

open TODOs for #60

  • define covariance for gquads in Algebras/alg_ali_purecovar.gap, Algebras/Probing/Parts/algpart_probing_gquad.gap
  • define hi_shape definitions in Algebras/Shapes/alg_ali_hishapes.gap and Algebras/Shapes/alg_hishapes.gap
  • check against RNAfold how probing parameters get applied to gquads in Algebras/Probing/Parts/algpart_probing_gquad.gap
  • how could gquads be integrated into macrostate pfunc computation? Algebras/Pfunc/alg_pfunc_macrostate.gap. gquad are not yet added to the macrostate grammar, probably for good
  • we might want to allow several mismatches for onlychar in alifold.hh and have this ratio as a parameter?!
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