Contents
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Deprecated Methods
does not handle corner cases
it is advised to use methods based on the ion type rather
than on the peak label
use the method based on the Ion class instead
used only in demo classes
from Comet release 2015.02 all searches use this internal
data representation by default
from Comet release 2015.02 all searches use this internal
data representation by default
use getMaxLoadedProteins and getMaxLoadedSpectra instead
use setMaxLoadedProteins and setMaxLoadedSpectra instead
use the decoy tag from FastaParameters instead
use the decoy tag from FastaParameters instead
Removed in Tide 4.2 (or earlier)
Removed in Tide 4.2 (or earlier)
use the getCvTerm method for the PTM instead
the CV term is now part of the PTM object
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Deprecated Constructors
use ProgressDialogX instead