haplotype frequency = (number occurrences) / (total observations) 

The "direct count" method haplotype frequency is literally an exact frequency of a haplotype in your observed samples, obtained by dividing the count of occurrences over total observations. To think about the "population" haplotype frequency, you could then consider this within a statistical framework. 

With missing data (for example you only have SNPs, and want to estimate the frequency of those SNPs co-occurring on the same chromosome in the population (="haplotype"), you would need to derive haplotype frequencies by considering the probability of different genotypes co-occurring. The most common algorithm, I think, for doing this is the expectation-maximization algorithm of Excoffier and Slaktin (1995), linked below. This can be done with the program Haploview, also linked. 

http://www.uvm.edu/~rsingle/stat380/F04/possible/Excoffier+slatkin-MolBiolEvol-1995.pdf

http://www.ibi.vu.nl/teaching/masters/seq_analysis/2005/litt/barret_et_al_2005.pdf

https://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview

If you are interested in an efficient way to count the number of haplotypes based on DNA sequence alignments, I would recommend DnaSP, which can also reconstruct haplotypes from unphase data using 3 alternative methods: PHASE 2.1 (a coalescent-based Bayesian methods by Stephens et al. 2001), fastPHASE1.1 a modified algorithm of Phase2.1 taking into account patterns of linkage disequilibrium by Sheet & Stephens 2006; HAPAR based on a parsimony approach by Wang & Xu 2003.

DnaSP incorporates these approaches and is freely available and also provides good documentation on use and underlying methods: http://www.ub.edu/dnasp/

Once you have the haplotype counts, it's pretty straightforward to figure out the frequencies as show by the equation provided in the previous answer by Tyler Chafin.

I hope this helps!

Cheers, Oliver