java changes String during processing?

i have to parse two large text-files. Each file contains a String-Mapping from a local-identifier to a String-value. The local-identifier is in fact just a temporary key. Later the mapping should be from value(file1) to value(file2).

so what i did was:

• build HashMaps with the mappings in every file.
• by iterating over the keyset i build a hashmap which maps value(file1) to value(file2)

after that i had three HashMaps

1. localid -> value(file1)
2. localid -> value(file2)
3. value(file1) -> value(file2)

What i did for verification was: for each localid

• a)get value(file1) out of Map 1
• b)get value(file2) out of Map 2
• c)get value(file2) out of Map3 with the key out of step a)
• d)compare value(file2)_b with value(file2)_c

what happens is that the two values in step d) are not equal in 15% of the key-value-pairs.

Actually there is some kind of System there... For example N2c changes into [N]2c, [nH]1c3c changes into n1c3c and (N) changes into ([NH])

is it possible that Java interprets the String as regular expressions or has anyone another idea?

thanks a lot

EDIT: ok here is some code^^ yeah this is more readable... sorry...

    HashMap<String, String> idToFile1 = File1.getMapping();
    HashMap<String, String> idToFile2 = File2.getMapping();

    HashMap<String, String> file1ToFile2 = new HashMap<String, String>();
    for(String localid : smilesfragments.keySet()){
        inchiToSmiles.put(idToFile1.get(localid), idToFile2.get(localid));
    }

    for(String localid : idToFile1.keySet()){
        String file1val  = idToFile1.get(localid);
        String file2val = idToFile2.get(localid);
        if(!file2val.equals(file1ToFile2.get(file1val))){
            System.err.println("mismatch!");
        }
    }

I get the mismatch in 15% of the cases