CHANGES IN VERSION 1.3.9
------------------------

    o Capitalisation aliases added for most functions.
    o The rtandem function now has an 'output.path' argument. 

BUG FIXES

    o Changed default parameters to prevent the risk of not generating output files.
    o Fixed a bug with 'rtandem()' where the function would not take a complex rTTAXO object as argument.


CHANGES IN VERSION 1.3.8
------------------------

BUG FIXES

    o Fixed a memory leak associated with PTMTreeSearch.
    o Removed an unwanted side-effect from the function GetPeptides().


CHANGES IN VERSION 1.3.7
------------------------

NEW FEATURES

    o rTANDEM now includes the PTMTreeSearch scoring algorithm.
    o New function to set default values for PTMTreeSearch algorithm.

CHANGES IN VERSION 1.3.5
------------------------

NEW FEATURES

    o New rTResult_s class support saving spectra.
    o New function 'ms2.plot' to visualize spectra.

CHANGES IN VERSION 1.3.4
------------------------

NEW FEATURES

    o rTANDEM now supports TPP's hrk-score function.

BUG FIXES

    o Fixed a bug with k-score function.

CHANGES IN VERSION 1.3.3
------------------------

NEW FEATURES

    o Functions have been implemented to create and manipulate parameter objects (S3 class rTParam). Those functions give default values for instrument-specific parameters for some types of mass spectrometer as well as default values for general parameters. 

CHANGES IN VERSION 1.3.2
------------------------

NEW FEATURES

    o rTANDEM now supports the k-score function. It can be used by setting the parameter 'scoring, algorithm' to "k-score".

CHANGES IN VERSION 1.1.6
------------------------

NEW FEATURES

    o rTANDEM is now based on x!tandem version 13-09-01 'sledgehammer'

CHANGES IN VERSION 1.1.5
------------------------

BUG FIXES

    o Fixed a memory management problen in Cpp

NEW FEATURES

    o More parameters are supported. 

CHANGES IN VERSION 1.1.4
------------------------

NEW FEATURES

    o rTANDEM is now based on x!tandem version 13-06-15 'jackhammer'

BUG FIXES

    o Corrected a bug that prevented the use of multi-threading
    o Corrected a bug that could affect results when multiple fasta files are assigned to a same taxon.
