#### Notes on the polysat GUI ####

This is not a comprehensive guide to polysat by any means!!  Refer to
the Tutorial Manual, Reference Manual, and Computer Program Note in
Molecular Ecology Resources for more information on the uses and
limitations of this R package.

### General advice

Keep the R console in view while working with the GUI.  Errors and
other important information will be printed to the console.  More
importantly, do not exit R while the GUI is running or it will not
work.

The 'Polysat Main Window' may appear small at first but can be resized
using the mouse.

"Save Project" does not automatically add a file extension.  Users
should add ".RData" to the end of these file names.  Likewise, ".txt"
can be added by user to the end of filenames for data export.

When you exit R and are given the choice to save the workspace image,
select "yes" unless you have a reason to discard your data and
results.  When the GUI is launched again, it will automatically detect a
previous project if there is one in the workspace.  This includes the
dataset (everything in the "genambig" object) as well as sample and
locus subsets and results.  All of this information can also be saved
to a separate file with the "Save Project" option.  Note that if you
export to a text file and then import that file back in to the GUI,
you will lose the sample and locus subsets and results, as well as some
aspects of the "genambig" object depending on the text file format.

### Moving between the GUI and the command-line

Objects that are created by the GUI can be accessed and edited by
command line and vice versa, even without closing the GUI.  The
objects created and used by the GUI are:
1.  genobject   A "genambig" object containing the genotypes,
                population names and identities, microsat repeat
                lengths, ploidies, and description.
2.  gsamples    A list of character vectors.  Each vector contains a
                set of sample names to be used for accessing subsets
                of data.  Each item in the list has a name that is
		used by the GUI.  By default the first item in the
		list is called "All" and contains all of the sample
		names.
3.  gloci       A list of character vectors, indicating subsets of
                loci the same way that 'gsamples' indicates subsets of
		samples.

### Minor notes

gUsatnts ("Edit Repeat Lengths"): if user previously selected
"Already expressed in
number of repeats", the next time the default button is going to be
"Mononucleotide repeats" because both give a value of 1.