DEPRECATED This parameter has been deprecated and is ignored in the current release of Kojak.
By default, Kojak uses a modified form of the Comet Xcorr algorithm. The modifications include a reduced data structure that is much more memory efficient, but produces slightly different Xcorr scores due to rounding differences during analysis. The default Kojak implementation works as the authors intended for analysis of cross-linked spectra. However, the original Comet algorithm persists for legacy and diagnostic purposes.
Using the Comet Xcorr is NOT recommended.
Setting this parameter to 1 enables Comet Xcorr. Setting this parameter to 0 uses the default Kojak implementation of the algorithm.
1.0 - 1.4.3 DEPRECATED
To enable the Comet Xcorr scoring algorithm:
use_comet_xcorr = 1