Begun work on the new HybRIDS reference class

Not yet finished - methods are not fully migrated over.
Created the DNA Sequence containing Reference Class

The HybRIDSseq reference class stores sequence information in memory
and the actual sequence in a file. Therefore accessing it only
temporarily takes up memory. It posesses a method to read in DNA
sequences from FASTA format.
Completed fully the DNAreference Object and the Triplet Reference Object, Finished the SSAnalyis Stage
Incorporated ggplot2 lineplot generation into HybRIDS Triplet Methods.
Finished Basic Rainbow Bar plotting method

Just needs a bit of refinement and provision for options such as titles
and legends.
Incorporated the putative bock finding process as a method of triplet R5 objects.
Finished Linesplotting for pair's of sequences.
Updated plotting methods - now pairs can be plotted with LinesPlots
Changed plotting to now get values from PlottingParams section of HybRIDS object.

Next job is to hook this into the plotSS method and passparameters to
the submethods. Modify the plotSS method to change parameters on the
fly.
Merge branch 'reference-class-implementation' into devel
Begun changes to plotting system