Commits · f1f24e1d5b8fd4a1f1e64ff7545b7f733c587f3b · Martin Larralde / pyhmmer · GitLab

01 May, 2022 4 commits
- Fix remaining small issues in documentation · f1f24e1d
  Martin Larralde authored May 01, 2022
  
  f1f24e1d
- Fix tests failing from the latest change in `repr` implementations · a051ea1d
  Martin Larralde authored May 01, 2022
  
  a051ea1d
- Implement `__str__` for `plan7.Alignment` using `p7_nontranslated_alidisplay_Print` · bf0494eb
  Martin Larralde authored May 01, 2022
  
  bf0494eb
- Add `__repr__` implementation to `pyhmmer.plan7.HMMFile` · 27bc3570
  Martin Larralde authored May 01, 2022
  
  27bc3570
29 Apr, 2022 1 commit
- Add disclaimer about name being required for `Builder.build_msa` · 7179f89e
  Martin Larralde authored Apr 29, 2022
  
  7179f89e
27 Apr, 2022 3 commits
- Fix `IterativeSearch` adding empty accessions for query missing one · c70c437b
  Martin Larralde authored Apr 27, 2022
  
  c70c437b
- Declare additional C variables in `IterativeSearch.__next__` · be3bba50
  Martin Larralde authored Apr 27, 2022
  
  be3bba50
- Fix methods used for manually controlling the inclusion of a `Hit` · e19d427e
  Martin Larralde authored Apr 27, 2022
  
  e19d427e
23 Apr, 2022 4 commits
- Make `HMMPressedFile.__init__` raise an exception when called · eef9c142
  Martin Larralde authored Apr 23, 2022
  
  eef9c142
- Rename `SearchIteration` to `IterationResult` for consistency · bcbecab5
  Martin Larralde authored Apr 23, 2022
  
  bcbecab5
- Add custom class to run iterative search queries against a HMMER daemon · 317e1bd3
  Martin Larralde authored Apr 23, 2022
  
  317e1bd3
- Add `select_hits` argument to iterative search methods of `Pipeline` · df08b4d7
  Martin Larralde authored Apr 23, 2022
  
  df08b4d7
22 Apr, 2022 7 commits
- Fix minor issues in the documentation of `pyhmmer.daemon` and the type... · 3839800d
  Martin Larralde authored Apr 22, 2022
```
Fix minor issues in the documentation of `pyhmmer.daemon` and the type annotations of `pyhmmer.plan7`
```
  3839800d
- Add `plan7.IterativeSearch` and `plan7.SearchIteration` to the documentation · 0fb777d6
  Martin Larralde authored Apr 22, 2022
  
  0fb777d6
- Add tests to verify `Pipeline.iterate_seq` results are consistent with `jackhmmer` · 5e99f84e
  Martin Larralde authored Apr 22, 2022
  
  5e99f84e
- Use a Cython namedtuple-style class for results in each `IterativeSearch` iteration · fd3bbf91
  Martin Larralde authored Apr 22, 2022
  
  fd3bbf91
- Rewrite iterative search as a dedicated iterator class · f67b8935
  Martin Larralde authored Apr 22, 2022
  
  f67b8935
- Add `Pipeline.iterate_seq` to run `jackhmmer`-style homology searches · 5b58f0e6
  Martin Larralde authored Apr 22, 2022
  
  5b58f0e6
- Add the `TopHits.compare_ranking` method to compare ranked hits to a previous run · 8289b4bc
  Martin Larralde authored Apr 22, 2022
  
  8289b4bc
21 Apr, 2022 6 commits
- Update `TopHits.to_msa` to support adding additional sequences to the alignment · 9b5e98d0
  Martin Larralde authored Apr 21, 2022
  
  9b5e98d0
- Add `Hit` methods to manually include or drop a hit · 6374f949
  Martin Larralde authored Apr 21, 2022
  
  6374f949
- Add `Trace.from_sequence` to create a faux trace from a single sequence with only matching states · 3710262a
  Martin Larralde authored Apr 21, 2022
  
  3710262a
- Add a constructor for individual `Trace` objects · 88e352c9
  Martin Larralde authored Apr 21, 2022
  
  88e352c9
- Make `plan7.Trace.posterior_probabilities` optional in case memory is not allocated · 3b7e123b
  Martin Larralde authored Apr 21, 2022
  
  3b7e123b
- Add setters for `Hit.name`, `Hit.accession` and `Hit.description` properties · b6858399
  Martin Larralde authored Apr 21, 2022
  
  b6858399
20 Apr, 2022 2 commits
- Fix `LongTargetsPipeline.arguments` not compiling · a3a724d8
  Martin Larralde authored Apr 20, 2022
  
  a3a724d8
- Add hints about corresponding binaries in `daemon.client` and `plan7.Pipeline` methods · 90a39ee4
  Martin Larralde authored Apr 20, 2022
  
  90a39ee4
19 Apr, 2022 2 commits
- Add `Pipeline.arguments` method to show a pipeline configuration as CLI flags · a4eff443
  Martin Larralde authored Apr 19, 2022
  
  a4eff443
- Move `P7_HIT` declaration and associated functions out of `p7_tophits.pxd` · 1a00560c
  Martin Larralde authored Apr 19, 2022
  
  1a00560c
14 Mar, 2022 2 commits
- Add `versionadded` directive to new `plan7.TopHits` properties [ci skip] · 01dd0716
  Martin Larralde authored Mar 14, 2022
  
  01dd0716
- Fix documentation of `pyhmmer.plan7.PipelineSearchTargets` · dc7caacb
  Martin Larralde authored Mar 14, 2022
  
  dc7caacb
03 Mar, 2022 1 commit
- Fix several uses of `memcpy` that could cause undefined behaviour · 4b96b0b5
  Martin Larralde authored Mar 03, 2022
  
  4b96b0b5
01 Mar, 2022 8 commits
- Overload `+` for `TopHits` to merge several top hits together · 1766ae2d
  Martin Larralde authored Mar 01, 2022
  
  1766ae2d
- Update `TopHits.merge` to support more than one argument · d73c0d70
  Martin Larralde authored Mar 01, 2022
  
  d73c0d70
- Bump `versionadded` directives to new minor version · c99c8b1a
  Martin Larralde authored Mar 01, 2022
  
  c99c8b1a
- Update management of pipeline parameters in `TopHits` code · 86909db4
  Martin Larralde authored Mar 01, 2022
  
  86909db4
- Fix erroneous debug assertion in `TopHits.copy` · b6efd78b
  Martin Larralde authored Mar 01, 2022
  
  b6efd78b
- Implement `TopHits.merge` to merge two collections of hits · 434b0c6a
  Martin Larralde authored Mar 01, 2022
  
  434b0c6a
- Update `TopHits` to store the method the `Z` and `domZ` parameters where obtained with · fe476bae
  Martin Larralde authored Mar 01, 2022
  
  fe476bae
- Implement `TopHits.copy` by manually copying all hits and domains · af5ec9a0
  Martin Larralde authored Mar 01, 2022
  
  af5ec9a0