def buildGrammar(self, grammar):
"""build PFold like grammar."""
Grammar.buildGrammar(self, grammar)
# state pfoldS
grammar.addRule(Rule(("pfoldS", ), ("pfoldL", ), ("prob", (1.0, ))))
grammar.addRule(Rule(("pfoldS", ), ("pfoldB", ), ("prob", (1.0, ))))
# state pfoldF
annotation1 = Annotation(row="PFOLD", column="LNUC", label="<")
annotation2 = Annotation(row="PFOLD", column="RNUC", label=">")
grammar.addRule(
Rule(("pfoldF", ), ("LNUC", "pfoldF*", "RNUC"),
gapsok=True,
annotations=[annotation1, annotation2]))
grammar.addRule(Rule(("pfoldF*", ), ("pfoldF", ), ("prob", (1.0, ))))
grammar.addRule(Rule(("pfoldF*", ), ("pfoldB", ), ("prob", (1.0, ))))
## state pfoldB
grammar.addRule(Rule(("pfoldL", ), ("pfoldF", ), ("prob", (1.0, ))))
grammar.addRule(Rule(("pfoldL", ), ("pfoldU", ), ("prob", (1.0, ))))
## state pfoldB
grammar.addRule(Rule(("pfoldB", ), ("pfoldL", "pfoldS")))
annotation3 = Annotation(row="PFOLD", column="NUC", label="_")
## state pfoldB
grammar.addRule(
Rule(("pfoldU", ), ("NUC", "pfoldU*"),
gapsok=True,
annotations=[
annotation3,
]))
grammar.addRule(Rule(("pfoldU*", ), (), ("prob", (1.0, ))))
def buildGrammar(self, grammar):
"""build PFold like grammar."""
Grammar.buildGrammar( self, grammar)
# state pfoldS
grammar.addRule( Rule( ("pfoldS",),
("pfoldL",),
("prob", (1.0,)) ) )
grammar.addRule( Rule( ("pfoldS",),
("pfoldB",),
("prob", (1.0,)) ) )
# state pfoldF
annotation1 = Annotation( row = "PFOLD",
column = "LNUC",
label = "<" )
annotation2 = Annotation( row = "PFOLD",
column = "RNUC",
label = ">" )
grammar.addRule( Rule( ("pfoldF",),
("LNUC", "pfoldF*", "RNUC"),
gapsok = True,
annotations = [annotation1,annotation2] ) )
grammar.addRule( Rule( ("pfoldF*",),
("pfoldF",),
("prob", (1.0,) ) ) )
grammar.addRule( Rule( ("pfoldF*",),
("pfoldB",),
("prob", (1.0,) ) ))
## state pfoldB
grammar.addRule( Rule( ("pfoldL",),
("pfoldF",),
("prob", (1.0,)) ) )
grammar.addRule( Rule( ("pfoldL",),
("pfoldU",),
("prob", (1.0,)) ) )
## state pfoldB
grammar.addRule( Rule( ("pfoldB",),
("pfoldL", "pfoldS") ) )
annotation3 = Annotation( row = "PFOLD",
column = "NUC",
label = "_" )
## state pfoldB
grammar.addRule( Rule( ("pfoldU",),
("NUC", "pfoldU*"),
gapsok = True,
annotations = [annotation3,]))
grammar.addRule( Rule( ("pfoldU*",),
(),
("prob", (1.0,)) ) )
def __init__(self, *args, **kwargs):
Grammar.__init__(self, *args, **kwargs)
def __init__(self, *args, **kwargs):
Grammar.__init__(self, *args, **kwargs)
