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

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.