Yes, the computation of the saturation indices (traditional Langelier and my Calcite Saturation Index) adjust the TA to compensate for CYA (and for borates as well). You can see a line below the data entry lines called "Carbonate Alkalinity" which is adjusted TA and essentially that is what is used in the calculations (directly for the Lagelier index, though for my CSI I use the calculated calcium and carbonate concentrations directly and they have built into them the effects of adjusted TA).
It's not really necessary to adjust for TA unless the CYA is quite high. After all, when the CYA is 30 ppm, the adjustment is only 10 ppm in TA which results in a tiny change in the saturation indices (0.03 difference if the TA is 100). I just do all the adjustments and go crazy with the calculations because I'm a nerd.
Richard
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