Graph processing in EMBOSS
==========================

In the beginning there was plplot, and it was not ideal but would have
to do.

Graphs were divided into 2 kinds:

xygraph:
x axis is (usually) sequence coordinates
y axis is data plotted against the sequence

Supported by the "-graph data" type.
Graph is built using graph calls, then plotted in a single call
Separate XYDisplay call to display the graph

Programs:

abiview
charge
cpgplot
dan
dotmatcher (graph too)
dottup (graph too)
findkm
freak
hmoment
iep
isochore
octanol
pepinfo
pepwindow
pepwindowall
pestfind
plotcon
plotorf
syco
tcode
tmap
wobble

graph:
any other graph, including histograms

graph is drawn a component at a time
May start again on a new page (e.g. prettyplot)
Separate GOpen call to start the graph
Ended by ajGraphClose or ajGraphCloseWin (both simply call GraphClose)
But GraphxyGeneral also calls GraphClose so we should modify these separately.

Programs:

banana
chaos
dotmatcher
dotpath
dottup
pepnet
pepwheel
polydot
prettyplot

For the Staden spin program, these are all ignored - they have a -data
option which causes spin to use xwindows and skip the spin graph
viewer.

The challenge is to make data files that spin can use.

Spin notes:

lib/spin2_emboss/emboss_utils.tcl has:

list_graph_types
list_file_formats


To change for spin2:

edit lib/spin2_emboss/acd2tcl.tcl
comment out the resetting of graph to xwindows
run create_emboss_files

then test a graph program (e.g. chaos)
the distributed version would open an xwindow
now it ... does nothing!

For spin, we need a modified create_emboss_files_spin1 to change files
in the spin_emboss/acdtcl directory instead.