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0.4.11
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@althonos althonos released this 15 Dec 01:38
· 642 commits to master since this release
v0.4.11
f76e844

Added

  • plan7.HMMFile.read method to read a single plan7.HMM from an plan7.HMMFile (instead of using next).
  • closed property on easel.SequenceFile, easel.MSAFile and plan7.HMMFile to mark whether a file object is closed.
  • plan7.HMMFile.is_pressed method to check whether a HMM file has associated pressed data.
  • plan7.HMMFile.optimized_profiles methods to read the plan7.OptimizedProfile entries in an plan7.HMMFile is there are associated pressed data available.
  • Getters for the name, accession, description, consensus, consensus_structure, evalue_parameters and cutoffs properties of a plan7.OptimizedProfile.
  • plan7.OptimizedProfile.__eq__ implementation to compare two optimized profiles.
  • __sizeof__ implementations for plan7.OptimizedProfile and plan7.Profile to get the allocated size of a profile.

Fixed

  • Double-free caused by the Cython cycle breaking feature on several view types (easel.Randomness, easel.Vector, easel.Matrix, plan7.Cutoffs, plan7.EvalueParameters, plan7.Offsets, plan7.Trace)
  • plan7.Hit.description using the pointer to the accession string erroneously, causing occasional NULL dereference.
  • plan7.OptimizedProfile.copy performing a shallow copy instead of a deep copy as expected.

Changed

  • pyhmmer.hmmer type annotations now explicit support for plan7.Profile or plan7.OptimizedProfile inputs where applicable.
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