RELEASE HISTORY OF THE "cleaver" PACKAGE
========================================

Version 1.47.1 [2025-10-14]:
- Move package to codeberg.org.

Version 1.41.3 [2024-04-24]:
- Add 3 different types of trypsin (as defined in PeptideMass): trypsin-high
  (identical to the current trypsin rule and to PeptideMass' "higher
  specificity"), trypsin-low (cleavage after K/R but not if followed by P),
  trypsin-simple (cleavage after K/R even if followed by P);
  The trypsin rule is identical to trypsin-high and will be kept for
  backward compatibility.

Version 1.41.2 [2023-12-03]:
- Add missing documentation for LysargiNase.

Version 1.41.1 [2023-11-30]:
- Add LysargiNase cleavage rule.

Version 1.35.1 [2022-08-31]:
- Fix: adapt vignette code to new UniProt.ws.

Version 1.27.1 [2020-06-05]:
- Fix cleavage rule for glutamyl endopeptidase in documentation
  Thanks to Mariia Chernigovskaya <mariia.chernigovskaya@medisin.uio.no> for
  reporting this error.

Version 1.25.1 [2019-12-30]:
- Add missing space in vignette.

Version 1.21.4 [2018-12-26]:
- Use "https" in hyperlinks (where possible).

Version 1.21.3 [2018-12-26]:
- Correct cleavage rules for "pepsin" and "pepsin1.3". According to the
  peptidecutter documentation "pepsin1.3" is more specific (cleaves at [FL])
  than "pepsin" (cleaves [FLWY]);
  see https://codeberg.org/sgibb/cleaver/issues/6 for details.
  Thanks to Jean Manguy <jean@manguy.eu> for reporting this error.

Version 1.21.2 [2018-11-03]:
- Convert vignette from Sweave to rmarkdown.
- Another try to fix links in manual pages to avoid WARNING on Windows.

Version 1.21.1 [2018-11-01]:
- Add my ORCID to the Author field in DESCRIPTION.
- Fix links in manual pages to avoid WARNING on Windows.

Version 1.15.1 [2017-06-08]:
- Don't consider the last aminoacid as cleavage site.
  `cleavageSites("ACK", custom="K")` results in `integer()` instead of `3` now.
  Thanks Apurva Hegde <ahegde@tgen.org> for reporting this issue.
- Remove superfluous "missedCleavages" argument in `cleavageSites`.

Version 1.13.2 [2017-02-14]:
- Use `expect_equal` instead of `expect_identical` to avoid failing of the
  `.revsequence` unit test on "toluca2" (Mac OS X Mavericks (10.9.5) / x86_64).
- Add "importFrom(stats, setNames)" to NAMESPACE.

Version 1.13.1 [2017-01-04]:
- Remove GPL headers from *.R files.
- Remove useless return calls.

Version 1.5.3 [2015-02-02]:
- Set taxId=9606 for UniProt.ws in vignette.

Version 1.5.1 [2015-01-24]:
- Add test case if number of cleavage sites is smaller than the number of
  allowed missed cleavages.

Version 1.3.8 [2014-09-28]:
- Use title case in the "Title:" field of the DESCRIPTION file.

Version 1.3.7 [2014-05-08]:
- Create an IRangesList using `split` instead of `lapply` in the
  cleavageRanges,AAStringSet-method is more than two times faster.

Version 1.3.6 [2014-05-03]:
- Add cleavageRanges method for character, AAString and AAStringSet.
- cleave,AAString returns an AAStringSet instead of an AAStringSetList object.
- Fix return value of cleavageSites,AAStringSet.

Version 1.3.5 [2014-04-30]:
- Fix defintion of cleavageSites,AAStringSet.

Version 1.3.4 [2014-04-30]:
- Add cleavageSites method for character, AAString and AAStringSet.

Version 1.3.3 [2014-04-28]:
- Avoid duplicated digest of peptides results in a hugh speed improvement and a
  hugh memory reduction (removes fix from 1.1.8 and partly reintroduces original
  algorithm).
- Remove memory test and "memoryThreshold" argument (fails on different
  platforms and is not important anymore using the "new" cleavage algorithm).
- Change default of "unique" argument to "unique=TRUE".

Version 1.3.2 [2014-04-25]:
- Introduce simple memory test and "memoryThreshold" argument to avoid the
  calculation of ridiculous high numbers of "missedCleavages" and peptide
  combinations.

Version 1.3.1 [2014-04-25]:
- Add "custom" argument to allow the user defining own cleavage rules.

Version 1.1.8 [2014-03-26]:
- Fix missedCleavages>1.
- Add argument "unique".
- Add methods, Biostrings, IRanges to NAMESPACE.

Version 1.1.7 [2014-03-25]:
- Typo in the manual page.

Version 1.1.5 [2014-02-25]:
- Using AAStringSetList constructor for list of characters instead of
  creating a lot of AAStringSets dramatically decreases running time for
  cleave,AAStringSet-method.

Version 1.1.4 [2013-12-20]:
- tests:
  - move tests into tests/testthat to adapt to testthat 0.8 and new
    CRAN policy.

Version 0.99.5 [2013-07-24]:
- vignette:
  - remove duplicated sessionInfo entries.

Version 0.99.4 [2013-07-23]:
- vignette:
  - use BiocStyle.
  - add sessionInfo() and TOC.

Version 0.99.3 [2013-07-08]:
- vignette: add second BRAIN reference.

Version 0.99.2 [2013-06-17]:
- Replace own AAStringSetList constructor by Biostrings::AAStringSetList.
- man/cleaver-package.Rd: remove static date.
- vignette: add dynamic date and don't load Biostrings manually anymore.
- NAMESPACE: don't import from Biostrings and IRanges.

Version 0.99.1 [2013-05-30]:
- Add S4-methods for character, AAString, AAStringSet.
- man/cleave-methods.Rd: split table of cleavage rules to reduce table width.
- Extend vignette (add BRAIN and UniProt.ws based examples).

Version 0.99.0 [2013-04-27]:
- Initial release.