comparing each lines from two different file

Well firstly we have two files , we have to create 2 list which do reads line of file. And after there should be some algortihm which compares those two files. Comparison is like that ; compare first 2 elements with two each elements of the second list here is an example 1: ABCDEFGHIJKLMN 2: OPRABSTUWXYZ first : AB AB - OP AB - PR AB - RA AB - AB OK but find only one not each so when we find AB in OPRABSABTUABWXYABZ it should find only the first AB, and only if we get AB again then find another one, not the same you can mark found ones with ** in front (highlighting) it should be done in java codes. reason for project is simply comparing two php codes for plagiaris and this is urgent..