def __init__(self):
MATCH_STATE = "MATCH_STATE"
GAP_STATEX = "GAP_STATEX"
GAP_STATEY = "GAP_STATEY"
self.xSeq = None
self.ySeq = None
self.xStart = None
self.yStart = None
self.stateMachine = SparseAlign.StateMachine()
self.stateMachine.addState(MATCH_STATE, self.match_de,
SparseAlign.StateMachine.MATCH)
self.stateMachine.addState(GAP_STATEX, self.gap_deX,
SparseAlign.StateMachine.GAPX)
self.stateMachine.addState(GAP_STATEY, self.gap_deY,
SparseAlign.StateMachine.GAPY)
self.stateMachine.addTransition(MATCH_STATE, MATCH_STATE,
self.transitionFn(MATCH))
self.stateMachine.addTransition(MATCH_STATE, GAP_STATEX,
self.transitionFn(GAP_OPEN))
self.stateMachine.addTransition(GAP_STATEX, MATCH_STATE,
self.transitionFn(GAP_CLOSE))
self.stateMachine.addTransition(GAP_STATEX, GAP_STATEY,
self.transitionFn(GAP_SWITCH))
self.stateMachine.addTransition(MATCH_STATE, GAP_STATEY,
self.transitionFn(GAP_OPEN))
self.stateMachine.addTransition(GAP_STATEY, MATCH_STATE,
self.transitionFn(GAP_CLOSE))
self.stateMachine.addTransition(GAP_STATEY, GAP_STATEX,
self.transitionFn(GAP_SWITCH))
self.startStates = [0, 0, 0] #Maths.NEG_INFINITY, Maths.NEG_INFINITY]
self.endStates = self.startStates[:]
self.diagTraceBackLimit = 1
global m, gapEmissions
m = [math.log(i) for i in m]
gapEmissions = [math.log(i) for i in gapEmissions]
i = [float(i) for i in open("gapDist", 'r').readlines()]
j = sum(i)
i = [math.log(k / j) for k in i]
self.gapDist = i
def __init__(self):
MATCH_STATE = "MATCH_STATE"
GAP_STATEX = "GAP_STATEX"
GAP_STATEY = "GAP_STATEY"
self.xSeq = None
self.ySeq = None
self.xStart = None
self.yStart = None
self.stateMachine = SparseAlign.StateMachine()
self.stateMachine.addState(MATCH_STATE, self.match_de,
SparseAlign.StateMachine.MATCH)
self.stateMachine.addState(GAP_STATEX, self.gap_de,
SparseAlign.StateMachine.GAPX)
self.stateMachine.addState(GAP_STATEY, self.gap_de,
SparseAlign.StateMachine.GAPY)
self.stateMachine.addTransition(MATCH_STATE, MATCH_STATE,
self.transitionFn(MATCH))
self.stateMachine.addTransition(MATCH_STATE, GAP_STATEX,
self.transitionFn(0.0))
self.stateMachine.addTransition(GAP_STATEX, MATCH_STATE,
self.transitionFn(0.0))
self.stateMachine.addTransition(GAP_STATEX, GAP_STATEY,
self.transitionFn(GAP_SWITCH))
self.stateMachine.addTransition(MATCH_STATE, GAP_STATEY,
self.transitionFn(0.0))
self.stateMachine.addTransition(GAP_STATEY, MATCH_STATE,
self.transitionFn(0.0))
self.stateMachine.addTransition(GAP_STATEY, GAP_STATEX,
self.transitionFn(GAP_SWITCH))
self.startStates = [0, 0, 0] #Maths.NEG_INFINITY, Maths.NEG_INFINITY]
self.endStates = self.startStates[:]
self.diagTraceBackLimit = 1
self.COMBINED = GAP_EMISSIONL + GAP_EXTEND
self.COMBINED2 = GAP_EMISSIONL + JUNK_EXTEND
MATCH = 0.9703833696510062
GAP_OPEN = (1.0 - MATCH) / 2
GAP_CLOSE = 1.0 - GAP_EXTEND - GAP_SWITCH
GAP_SWITCH = 0.0007315179552849
match_match_t = transitionFn(MATCH)
match_gap_t = transitionFn(GAP_OPEN)
gap_match_t = transitionFn(GAP_CLOSE)
gap_gap_t = transitionFn(GAP_SWITCH)
"""
end space for parameters
"""
stateMachine = SparseAlign.StateMachine()
stateMachine.addState(MATCH_STATE, de, SparseAlign.StateMachine.MATCH)
stateMachine.addState(GAP_STATE, de, SparseAlign.StateMachine.GAP)
stateMachine.addTransition(MATCH_STATE, MATCH_STATE, t)
stateMachine.addTransition(MATCH_STATE, GAP_STATE, t)
stateMachine.addTransition(GAP_STATE, MATCH_STATE, t)
stateMachine.addTransition(GAP_STATE, GAP_STATE, t)
startStates = [0, Maths.NEG_INFINITY]
endStates = startStates[:]
def diagBuilder(i, j):
raise NotImplementedError("Shouldn't be called")
