> Well, I’m a computer scientist student and as a part of my final
> degree project I need to solve the well-known Travelling Salesman
> Problem with several complications added.

Search this group for 'TSP', it seems to be a popular project.
Sample discussion -
  
http://groups.google.com/group/Google-Maps-API/browse_thread/thread/21e857c2a506883d/3b2f5b19d758174f?lnk=gst&q=tsp#3b2f5b19d758174f

> I reading the points from a file which has a lot of points and my
> problem is that I can't get the distance between each point when I
> have more than 27 points.

That's the practical issue that directions requests are deliberately
throttled to discourage abuse.
Starter on handling that -
  http://econym.org.uk/gmap/geomulti.htm
whch is about geocoding, but the same principles apply to directions.

cheers, Ross K
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