Add support for per-cell setting of the inhibited flag in chain configuration

[churli]

With chain configuration files we can specify if a chan is inhibited or permissible to transcriptional activation.
We would like to be able to specify the inhibition flag also at the single-cell level, so that a chain can be composed to both permissible and inhibited elements.

[churli]

This feature requires changes in both active-microemulsion and chainConfigurator.py, for reading and producing the chain config files respectively.
The syntax specification (initally from Issue #6 ) should be amended so that the initial parameter of a step is the permissibility flag.

[churli]

Syntax specification has therefore been changed to:

CHROMATIN,Active=boolFlag,Transcribable=boolFlag,Inhibited=boolFlag,Cutoff=boolFlag : (x0,y0) : multiplier(permFlag,xStep,yStep) ...
where:

• boolFlag: can be either 0 or 1.
• multiplier: is a positive integer specifying how many times the step should be repeated.
• permFlag: is either "p" (permissible) or "i" (inhibited).
• xStep/yStep: are signed integers specifying the step to take. Expected values are "+1", "0", "-1". "+" and "-" values are also accepted as aliases of "+1" and "-1" respectively.
• Cutoff: the cutoff flag specifies if the chain should be affected by the cutoff conditions changes.

e.g.:
CHROMATIN,Active=0,Transcribable=0,Inhibited=0,Cutoff=1 : (1,1) : 49(p,+,0) 2(i,0,+) 49(i,-,0) 2(p,0,+) ...