Version 1.9.1
________________________________________________________________________________
* Move example files into package to avoid spurious check errors in windows

Version 1.7.1
________________________________________________________________________________
* Imports generics from ProtGenerics
* Export base classes

Version 1.5.3
________________________________________________________________________________
* Use "location" attribute instead of "name" to create the
  spectrumFile/databaseFile column in the flattened data.frame.

Version 1.3.6
________________________________________________________________________________
* Huge restructuring in documentation
* Fixed a bug that would throw an error when an empty mzID object was flattened
* Restructuring of unit tests so they conform with 'new' guidelines and gets
  called during check

Version 1.3.5
________________________________________________________________________________
* Bug fixes

Version 1.3.4
________________________________________________________________________________
* Bug fixes

Version 1.3.3
________________________________________________________________________________
* Added method removeDecoy, to remove decoy specific information from an mzID or
  mzIDCollection object thus decreasing its size.
* Added formal getter methods to extract specific information from mzID and
  mzIDCollection objects
* All attribute names are now parsed as-is despite inconsitency between schema
  versions. Controlling compatability is now done using the safeName parameter 
  in flatten and getter methods
* Substantial cleanup in documentation

Version 1.3.2
________________________________________________________________________________
* Fixed bug due to R's change in type.convert() that would result in precise 
  numbers being reported as strings

Version 1.3.1
________________________________________________________________________________
* Fixed bug that would cause error on files with no modifications in the search
  parameters

Version 1.2
________________________________________________________________________________
* Release on Bioconductor

Version 1.1.6
________________________________________________________________________________
* Added documentation

Version 1.1.5
--------------------------------------------------------------------------------
* Now computes mzR compatible acquisitionNum for the scans (thanks to Sebastian
  Gibb)
* Checks for existence of local files (thanks to Sebastian Gibb)
* XML moved from depend to import

Version 1.1.4
--------------------------------------------------------------------------------
* Now computes mzR compatible acquisitionNum for the scans (thanks to Sebastion
  Gibb)
* Various bug fixes

Version 1.1.3
--------------------------------------------------------------------------------
* Introducing the mzIDCollection class to handle multiple mzID objects

Version 1.1.2
--------------------------------------------------------------------------------
* Added the possibility to create the different 'sub'classes of mzID directly
  from a file without first having an internal xml representation and namespace

Version 1.1.1
--------------------------------------------------------------------------------
* Fixed bug where multiple names in the modification rules would crash the
  parsing. Multiple names gets collapsed with '/'

Version 1.0.0
--------------------------------------------------------------------------------
* Accepted in Bioconductor

Version 0.99.3
--------------------------------------------------------------------------------
* Fix for issue #6. It now correctly parses files with empty AnalysisData
  nodes as empty mzID objects.
* Full support for mzIdentML v1.0 and v1.1 

Version 0.99.2
--------------------------------------------------------------------------------
* Accepted in Bio 2.13

Version 0.9.1
--------------------------------------------------------------------------------
* Added unit test using testthat for low level functions
* Added BiocViews DataImport, MassSpectrometry, Proteomics

Version 0.9.0
--------------------------------------------------------------------------------
* Submitted to Bioconductor

Version 0.3.1
--------------------------------------------------------------------------------
* Comment unused functions <2013-07-05 Fri>
* Minor typos in vignette  <2013-07-05 Fri>

Version 0.3.0
--------------------------------------------------------------------------------

NEW FEATURES AND FUNCTIONS
* Support for mzIdentML v1.0 (thanks Laurent Gatto)

Version 0.2.1
--------------------------------------------------------------------------------

NEW FEATURES AND FUNCTIONS
* Version counter now in BioConductor style
* Namespace now extracted from file instead of hardcoded in the constructor
* mzID constructor now checks the mzIdentML version before parsing (only 1.1.0
  supported atm)


Version 0.1-1
--------------------------------------------------------------------------------

NEW FEATURES AND FUNCTIONS
* Added function `flatten` to create tabular representation of results

Version 0.0-2
--------------------------------------------------------------------------------

NEW FEATURES AND FUNCTIONS
* The package is now fully documented
* created helper functions: `countChildren`, `attrExtract` and
  `attrExtractNameValuePair`
* Added NEWS file
* Added README.md file
* The parser now succesfully imports all test files on the HUPO mzIdentML page

PERFORMANCE
* Improvements in the mzIDpsm constructor makes it ~2-3x faster depending on the
  file size (thanks to `countChildren`, `attrExtract` and
  `attrExtractNameValuePair`)

Version 0.0-1
--------------------------------------------------------------------------------

NEW FEATURES AND FUNCTIONS
* First build of the package
* Introduction of the classes: `mzID`, `mzIDdatabase`, `mzIDevidence`,
  `mzIDparameters`, `mzIDpeptides` and `mzIDpsm` with related constructors
