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