CnvWrapper is a facade for Combined_CNV written by Stephan Sanders and Christopher Mason
it uses a Java interface to provide simple and intuitive commands that are backed by the perl script.
Constructor for CnvWrapper,
this code also contains the startup information for each proces in the menu,
to add a new function, simply follow the form below
PopWindow is an extension of the JDialog class and is an instance
of a pop up box that allows for the user to input required fields for
CombinedCNV after the input button is pressed, the PopWindow will close
and write to the log.txt file any commands inputted.
constructs an instance of PopWindow, the only real work
that needs to be done, the PopWindow parent CnvWrapper is used
to write out and call perl, and it works like a charm
the array log is used to determine the number of inputs and varies as per
the Combined_CNV function that needs to be done.
runPerl is used to write a specified command to the log.txt file,
and then to call the perlscript Combined_CNVvonline2.pl which reads
and feeds off of this log.txt file