Moving imports to their own namespace
Basic testing working on the cleanup
Splitting up monolithic code file
Adding in start of tools for network analysis
Fix search for common pathways
Can be generalised out to any number of gene sets now
Merge pathway searching methods
Namespace all the network code
Fixes to make sure the scale shows up on plots

Continue onwards with the really hacky colour
scale that we use to mark out each of the
different types of expression value.
Fixes for labelling of proteins with names/symbols
More of basics getting the plots working
Add in legend for GO plot
Update all the imports for the project
Export method
Remove the importFrom statements

We don't really need to use them, since we are
namespacing all the method calls anyway. There
were some Bioconductor libraries that ended up
trying to load up some of their dependencies when
attached, so it made the use of importFrom impossible
More documentation
Add in docs for calculateSequenceWindow
Documentation for domain sets
More doco
Pass on options to read.delim from download

We want to be able to pass on the options to read.delim, just
in case there are comment lines within the file
Doco and fixes for the gene ontology tools