Development

Created by: larsyunker

Fixed assumption that first mzML function number is 1.

• The default function is assigned as the minimum function number in the mzml. This may cause some problems in the future, but keyword passthrough should allow users to avoid those problems.
• Several passthroughs have been added to allow user specification of function.
• Any use of mzML functions has now been consistently labelled with the function keyword and variable

A couple of minor bug fixes and docstring updates as well.