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NEWS
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NEWS
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Version 0.0.8
________________________________________________________________________________
* prepareMethods handles scan preprocessing. Preprocessing is accessed using
prepareScans.
* Added localMax as a very simple centroiding algorithm.
* Added ionFilter as a simple filtering mechanism for ions in centroided scans
* Added methodStore as a virtual refclass that all methodstores should subclass
* MsConnections can now write modified scans and transparently extract the right
ones.
* Handling of raw vs. modified data. All raw extraction methods now have a raw
parameter to choose whether to extract directly from mzR connection. The
nature (raw vs unraw) is saved in the MsList object and passed on to
derivatives.
* Added isRaw to test whether elements are from raw data
* Added uNames to create truly unique names even with duplicate elements
* Added memberIndex and raw to the mapping matrix in MsList. raw saves the
rawness of the elements, memberIndex is in preparation to include MsDataSet as
connections instead of only MsData.
Version 0.0.7
________________________________________________________________________________
* Fully implemented MsPeakList with 2d and 3d plot
* Added filter family of functions to abstract sql queries
* Added limit familiy of functions to limit the number returned from queries
* Added MsDataSet class to handle a collection of MsData objects
* All MsList subclasses now have scans, chroms, ions and peaks methods
* MsList now contains MsData objects instead of MsConnections
* names method for MsList dynamically creates unique names
Version 0.0.6
________________________________________________________________________________
* Added peakMethodStore class to handle peak detection algorithms
* Added modified version of massifquant from xcms
* Huge improvements to MsIonList 2d plot
* Add precursor markers on MsScanList plot
Version 0.0.5
________________________________________________________________________________
* Added filtering options for MsData scans method
* Added XIC functionality to chroms method
* Added scans method to MsChromList class
* Added MsIonList class for handling raw ion measurements in a defined area
Version 0.0.4
________________________________________________________________________________
* Added README
* Begun the vignette
* Added MsChromList class and base methods
* Set up package for Rcpp
* Added getXIC Rcpp function
Version 0.0.3
________________________________________________________________________________
* Added MsList virtual class and MsScanList which subclasses it.
* Added standard functionality to both of the above classes
Version 0.0.2
________________________________________________________________________________
* Bug fixes
* Added documentation
* Add history table to sary
Version 0.0.1
________________________________________________________________________________
* First build
* Definition of MsData and MsConnections classes together with constructor
functions.
* Initial format for sary file defined