Add support for config-file-based chain initialization.

[churli]

The file should define a chain in each line in the following format: [ChemicalSpecies,Activity][Transcribability,Inhibition] (x0,y0)(xstep,yStep)... E.g.: [CHROMATIN,NOT_ACTIVE][NOT_TRANSCRIBABLE,POSSIBLE] (10,10)(+,0)(0,-)(+,+)(-,0)...

[churli]

Syntax specification has been changed to:

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

• boolFlag: can be either 0 or 1
• multiplier: is a positive integer specifying how many times the step should be repeated
• 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(+,0) 2(0,+) 49(-,0) 2(0,+) ...