CHANGES IN VERSION 0.25.1
-------------------------
 o Removing mapping functions, moved to the ensembldb package. <2019-08-08 Thu>
 o Marking package for deprecation <2019-08-08 Thu>

CHANGES IN VERSION 0.15.3
-------------------------
 o Working up new API (see issue #41) <2017-04-09 Sun>
 o Temporarily remove some vignettes, until the API has
   stabilised. <2017-04-09 Sun>

CHANGES IN VERSION 0.15.2
-------------------------
 o New Proteins class implementation - see issue #38. <2016-12-10 Sat>
 o Fixed many errors from current rewrite <2017-04-08 Sat>

CHANGES IN VERSION 0.15.1
-------------------------
 o Proteins,EnsDb method allowing to fetch a Proteins object from an EnsDb
   database.
 o Fixes in the mapToGenome method:
   - Works also for negative strand encoded proteins (issue #29).
   - Supports a GRangesList object with arbitrary mcols.
   - Faster implementation (issue #30).
 o mapToGenome,Proteins,EnsDb and pmapToGenome,Proteins,EnsDb methods that
   map peptide features to the genome using annotations fetched from an EnsDb.
 o The seqnames of the Proteins object are used as names for the resulting
   GRangesList object from the mapToGenome and pmapToGenome methods (issue #34).

CHANGES IN VERSION 0.15.1
-------------------------
 o Drop unique `seqnames` requirement; see #28, #32
 o Create `names` as synonym for `seqnames`; close #32

CHANGES IN VERSION 0.13.3
-------------------------
 o Update mapping vignette index entry, as suggested by Mike Love
   <2016-09-13 Tue>

CHANGES IN VERSION 0.13.0
-------------------------
 o Bioc devel

CHANGES IN VERSION 0.11.3
-------------------------
 o acols and pranges replacement method <2016-02-22 Mon>

CHANGES IN VERSION 0.11.2
-------------------------
 o add addPeptideFragments; see #24 for details [2016-02-07 Sun]

CHANGES IN VERSION 0.11.1
-------------------------
 o elementLengths was renamed -> elementNROWS in S4Vectors (new name
   reflects TRUE semantic, old name will be deprecated soon) [r113044
   | hpages@fhcrc.org | 2016-01-29 01:22:03 +0000 (Fri, 29 Jan 2016)]

CHANGES IN VERSION 0.11.0
-------------------------
 o New Bioc devel version

CHANGES IN VERSION 0.10.0
-------------------------
 o New Bioc release version

CHANGES IN VERSION 0.9.1
------------------------
 o update cleave method to address build error [2015-10-13 Tue]

CHANGES IN VERSION 0.9.0
------------------------
 o Bioc devel 3.2

CHANGES IN VERSION 0.8.0
------------------------
 o Bioc release 3.1

CHANGES IN VERSION 0.6.13
-------------------------
 o Updating Biomart query to reflect changes [2015-04-06 Mon]

CHANGES IN VERSION 0.6.12
-------------------------
 o Fix filling in tracks plots [2015-03-07 Sat]

CHANGES IN VERSION 0.6.11
-------------------------
 o Documentation for the plotting heler functions [2015-02-28 Sat]

CHANGES IN VERSION 0.6.10
-------------------------
 o plotting helper functions [2015-02-28 Sat]
 o fixed peptide grouping [2015-02-28 Sat]

CHANGES IN VERSION 0.6.9
------------------------
 o Fixing junction peptides splitting to support peptides reaching > 2
   exons [2015-02-27 Fri]
 o supporting more protein coding biotypes [2015-02-27 Fri]
 o rewrite and simplify proteinCoverage; closes #19 [2015-02-27 Fri]

CHANGES IN VERSION 0.6.8
------------------------
 o fix splitting exon junction ranges [2015-02-26 Thu]

CHANGES IN VERSION 0.6.7
------------------------
 o The genomic coordinates of peptides that overlap exon junctions are
   now correctly split instead of spanning over the exon and are
   grouped accordingly. [2015-02-26 Thu]

CHANGES IN VERSION 0.6.6
------------------------
 o update mapping vignette and use alignment to identify correct
   transcript [2015-02-25 Wed]

CHANGES IN VERSION 0.6.5
------------------------
 o see also mapping vignette in ?mapToGenome [2015-02-20 Fri]
 o calculateHeavyLabels, isCleaved, proteotypic and proteinCoverage
   are is now a function [2015-02-20 Fri]
 o added accessors to Pbase:::pplot() and update Pbase-data vignette
   accordingly [2015-02-21 Sat]

CHANGES IN VERSION 0.6.4
------------------------
 o typos in man [2015-02-19 Thu]
 o Added use.names argument ot etrid2gel [2015-02-19 Thu]
 o mapToGenome,Proteins,GRangesList (remove GRanges) using names for
   1-to-many mapping and document in mapping vignette [2015-02-19 Thu]

CHANGES IN VERSION 0.6.3
------------------------
 o new fig in Pbase-data vignette [2015-02-14 Sat]
 o new section for pmapToGenome in mapping vignette [2015-02-14 Sat]

CHANGES IN VERSION 0.6.2
------------------------
 o Add uniprot release to p metadata [2015-02-14 Sat]
 o added a metadata update method [2015-02-14 Sat]

CHANGES IN VERSION 0.6.1
------------------------
 o [p]mapToGenome methods [2015-02-14 Sat]

CHANGES IN VERSION 0.6.0
------------------------
 o fixed typos in vigs [2015-02-12 Thu]
 o new etrid2grl function to convert Ensembl transcript identifiers to
   GRangesList objects [2015-02-13 Fri]
 o initial mapToGenome function [2015-02-13 Fri]
 o regenerated p data using latest UniProt release and added
   acols(p)$ENST [2015-02-13 Fri]

CHANGES IN VERSION 0.5.5
------------------------
 o various fixes in vignettes [2015-02-12 Thu]

CHANGES IN VERSION 0.5.4
------------------------
 o Ensembl - UCSC mapping vignette [2015-02-11 Wed]

CHANGES IN VERSION 0.5.3
------------------------
 o Render vignettes with rmarkdown [2015-02-11 Wed]
 o Improve mapping vignette [2015-02-11 Wed]

CHANGES IN VERSION 0.5.2
------------------------
 o Adapt to new `addIdentification` signature in MSnbase >= 1.15.5.
   [2015-02-10 Tue]

CHANGES IN VERSION 0.5.1
------------------------
 o Update vignette since TxDb's UCSC coordinates differ from those
   fetched from Ensembl via biomaRt. [2015-01-05 Mon]
 o Add `isCleaved` method. [2015-01-03 Sat]
 o Add `calculateHeavyLabels`; closes #6 and cleaver#5. [2015-01-03 Sat]

CHANGES IN VERSION 0.5.0
------------------------
 o Bump version for new Bioc release.

CHANGES IN VERSION 0.2.2
------------------------
 o Fix warning re undocumented '[' and siglist 'Proteins,ANY,ANY,ANY'
   [2014-10-03 Fri]

CHANGES IN VERSION 0.2.1
------------------------
 o Counting id files when adding [2014-09-17 Wed]

CHANGES IN VERSION 0.2.0
------------------------
 o support for mzID and mzR (new) to extract identification data from
   mzid files via addIdentificationData [2014-09-12 Fri]
 o support to add id data from > 1 mzid file [2014-09-12 Fri]
 o new Pparams parameter infrastructure [2014-09-13 Sat]

CHANGES IN VERSION 0.1.10
-------------------------
 o Allow spaces in GeneNames (GN) of fasta comments; fixes #7 [2014-09-13 Sat]

CHANGES IN VERSION 0.1.9
------------------------
 o Use BioStyle

CHANGES IN VERSION 0.1.8
------------------------
 o Using knit2html instead of rmarkdown::render since it is not yet
   available on the Bioc build servers [2014-07-24 Thu]

CHANGES IN VERSION 0.1.7
------------------------
 o export vignettes [2014-07-22 Tue]

CHANGES IN VERSION 0.1.6
------------------------
 o New mapping vignette [2014-07-17 Thu]
 o Raw MSMS data pms data [2014-07-17 Thu]

CHANGES IN VERSION 0.1.5
------------------------
 o new data object p and vignette [2014-07-15 Tue]

CHANGES IN VERSION 0.1.4
------------------------
 o Fixed issues with proteins without any identifications in
   addIdentification Data; see also rmEmptyRanges functions to remove
   such proteins [2014-07-14 Mon]

CHANGES IN VERSION 0.1.1
------------------------
 o add biocViews and update README [2014-06-09 Mon]

CHANGES IN VERSION 0.1.0
------------------------
 o Added basic Proteins class [2014-05-02 Fri]
