NEWS

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mzID 1.9.1

• Move example files into package to avoid spurious check errors in windows

mzID 1.7.1

• Imports generics from ProtGenerics
• Export base classes

mzID 1.5.3

• Use "location" attribute instead of "name" to create the spectrumFile/databaseFile column in the flattened data.frame.

mzID 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

mzID 1.3.5

• Bug fixes

mzID 1.3.4

• Bug fixes

mzID 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

mzID 1.3.2

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

mzID 1.3.1

• Fixed bug that would cause error on files with no modifications in the search parameters

mzID 1.2

• Release on Bioconductor

mzID 1.1.6

• Added documentation

mzID 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

mzID 1.1.4

• Now computes mzR compatible acquisitionNum for the scans (thanks to Sebastion Gibb)
• Various bug fixes

mzID 1.1.3

• Introducing the mzIDCollection class to handle multiple mzID objects

mzID 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

mzID 1.1.1

• Fixed bug where multiple names in the modification rules would crash the parsing. Multiple names gets collapsed with '/'

mzID 1.0.0

• Accepted in Bioconductor

mzID 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

mzID 0.99.2

• Accepted in Bio 2.13

mzID 0.9.1

• Added unit test using testthat for low level functions
• Added BiocViews DataImport, MassSpectrometry, Proteomics

mzID 0.9.0

• Submitted to Bioconductor

mzID 0.3.1

• Comment unused functions <2013-07-05 Fri>
• Minor typos in vignette <2013-07-05 Fri>

mzID 0.3.0

NEW FEATURES AND FUNCTIONS

• Support for mzIdentML v1.0 (thanks Laurent Gatto)

mzID 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)

mzID 0.1-1

NEW FEATURES AND FUNCTIONS

• Added function 'flatten' to create tabular representation of results

mzID 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')

mzID 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