How can we calculate sea distances using waypoints?

I have one query in which I really stuck at that. I have port database with waypoints and also routing points which I need to use in distance calculation between two ports. I have done lots of R&D to find formula which gives me distance between two points. I also need shortest route which is possible.

I have reviewed online tools which allow user to calculate the distance. But I want to do the same at my own. I have reviewed Port World Distance Calculator. I reviewed the Great Circle formula to achieve that but I don't know that how we avoid landscapes in sea distance a开发者_Python百科nd in which direction I need to find distance for second port.

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The simpliest that comes - just create a table in your database like:

port1id : port2id : distance

number of ports are limited, and this table will give you flexibility to set correct distance