I was looking at an app on blackberry app world to create pdf files and that app claims to be able to password protect the files. How does one password protect a file. Isn't the code to read the file available, thus the password will be useless if the program decides not to check the password?
In addition to the other answers (which focus on encryption of arbitrary files) here an answer focusing on encryption of PDFs which was the use case initially startling the OP:
The PDF standard (ISO 32000-1) describes in section 7.6 how PDFs shall be encrypted in a manner that keeps the file structure of a PDF while hiding the content. PDFs are built from numerous objects (numbers, strings, arrays, dictionaries, streams, references, ...) and the mechanism described by the specification essentially only encrypts strings and stream contents.
Just like in the generic case described e.g. by @Mark, these encrypted string and stream contents are merely a bunch of random-looking data and have to be decrypted before the PDF can be displayed, but the remaining objects are unencrypted allowing PDF viewers and editors to recognize the file as a PDF.
Furthermore the PDF specification allows for two basic encryption types, by
Encryption using the latter kind of password obviously can be circumvented: After all, if you can view the PDF, you can extract all the data and do essentially what you want with unless your software co-operates with the scheme and forbids you to. And, obviously, not all software does co-operate.
Essentially the owner password mechanism stores a value in the PDF derived from the password which is sufficient to decrypt the encrypted data but does not allow for easy calculation of the original password.
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