Hide AA and Codon changes from zmenu when not known. RT #274986
Layout tweaks to difference track.
Three off-by-one errors caused by one-based co-ordinate system.
Fix start and end glyphs to be able to use rest of image.
This commit was manufactured by cvs2svn to create branch 'branch-
ensembl-68'.

Cherrypick from master 2012-07-27 11:55:33 UTC Beth Yates <bp1@sanger.ac.uk> 'better way to draw the Primary assembly alignment track on patch regions':
    modules/Bio/EnsEMBL/GlyphSet/patch_ref_alignment.pm
fix to not display if no features are present
clean up code
remove warns
Added support for fixed range graphs
Grey scale changed to run from white to black, and to allow max of range
to be specified
Added support for viewLimits to specify fixed range for graph
Added support for rendering as greyscale map rather than graph
Added support for optionally turning off zmenus on graph - was making page
load slow for Encode hub
Changed to using score rather than coverage for wiggle features
Use black as colour if can't get a sensible r,g,b colour from bigbed file
cutoffs for pig annotation status bands are different to zfish
Changes to make format->style call more efficient by using existing
BigBedAdaptor