modify definitions(for more high performance and safety)

[Giemsa]

Some member functions are called with call by value, in spite of using vector. I altered some method definitions for passing reference of vector, and added const to parameters to use more safely.

[jhasse]

Hi!

Thanks for the pull request, there are some very good changes in there :)

Before I merge this, can you have a look at my comments?

[Giemsa]

Thank you for looking my changes. I fixed some problems. Could you check my changes again?

[jhasse]

Looks good now :)

Thanks!