Comparing two files with the i-net PDFC API is quite simple. Just create a PDFComparer instance, start the comparison and assign the result to a local variable.
ResultModel result = new PDFComparer().compare( <file1>, <file2> );
Now, to get the total differences of all types, just call
int differences = result.getDifferencesCount( false )
With the boolean parameter of getDifferencesCount() you may activate the filter for certain types of differences. The filter is set by setTypeVisible() with a default visibility for all types of true.
Please note that there are a lot of additional API features to configure the comparison and to present the result.