Use 0-indexing for proteins/calculations.

I don't have confirmation that these changes will make the calculations
accurate, since I don't see the updated tests on Piazza just yet; however,
these changes are needed to make the proteins section work. Please review
and let me know if there is anything unexpected in this commit.
Added a "+1" to feature.toStr()'s start.

I can't actually find anywhere in the program that we are showing the user indices, other than in code from the first program which already does this.  Please point me to the code section that needs to print start indices to the user if I am mistaken.
Merge pull request #15 from mitchellwrosen/indexby0

Use 0-indexing for proteins/calculations.