def countsOnAlignment(qXa):
countsTotal = np.zeros((5,5))
countsTotalEmm = np.zeros((4,4))
transTotal = np.zeros((3,3))
gammaTotal = np.zeros((3))
alnQ,alnT = qXa[1],qXa[0]
nq = len(alnQ)
q = np.arange(nq,dtype=np.int_)
tempQ = map(ord,alnQ)
q = np.asarray(tempQ)
nt = len(alnT)
t = np.arange(nt,dtype=np.int_)
tempT = map(ord,alnT)
t = np.asarray(tempT)
countsLocal,transLocal,countsLocalEmm,gammaLocal = cS.getCountsFromAln(q,nq,t,nt)
countsTotal = np.add(countsLocal,countsTotal)
countsTotalEmm = np.add(countsLocalEmm,countsTotalEmm)
transTotal = np.add(transLocal,transTotal)
gammaTotal = np.add(gammaLocal,gammaTotal)
print "countsTotal:\n",countsTotal
tProb = cS.getTransProb(transTotal)
print "tProb:\n",tProb
ProbInit = cS.getInitProb(gammaTotal)
print "InitProb:\n", ProbInit
eProbM = cS.new_eProb(countsTotal)
print "eProb in match state:\n",eProbM
eProbX = cS.new_eProb(countsTotalEmm)
print "eProb in ins state:\n",eProbX
def countsOnList(SqPq):
countsTotal = np.zeros((5,5))
countsTotalEmm = np.zeros((4,4))
transTotal = np.zeros((3,3))
gammaTotal = np.zeros((3))
for hit in SqPq:
if hit != '':
alnQ,alnT = hit[1],hit[0]
nq = len(alnQ)
q = np.arange(nq,dtype=np.int_)
tempQ = map(ord,alnQ)
q = np.asarray(tempQ)
nt = len(alnT)
t = np.arange(nt,dtype=np.int_)
tempT = map(ord,alnT)
t = np.asarray(tempT)
countsLocal,transLocal,countsLocalEmm,gammaLocal = cS.getCountsFromAln(q,nq,t,nt)
countsTotal = np.add(countsLocal,countsTotal)
countsTotalEmm = np.add(countsLocalEmm,countsTotalEmm)
transTotal = np.add(transLocal,transTotal)
gammaTotal = np.add(gammaLocal,gammaTotal)
# print "countsTotal:\n",countsTotal
#print "countsTotalEmm:\n",countsTotalEmm
tProb = cS.getTransProb(transTotal)
# print "tProb:\n",tProb
tProb = balancetProb(tProb)
# print "tProbB:\n",tProb
ProbInit = cS.getInitProb(gammaTotal)
# print "ProbInit:\n",ProbInit
ProbInit = balanceProbInit(ProbInit)
# print "ProbInitB:\n",ProbInit
temp = np.vstack((tProb,ProbInit))
colOfZero = np.zeros((4,1))
temp2 = np.hstack((temp,colOfZero))
tau = np.array([[0.0],[0.0],[0.0],[0.0]])
temp3 = np.hstack((temp2,tau))
rowOfZero = np.zeros((1,5))
tProbHmm = np.vstack((temp3,rowOfZero))
# print "Transition Prob.:\n",tProbHmm
eProbM = cS.new_eProb(countsTotal)
# print "eProb in match state:\n",eProbM
eProbX = cS.new_eProb(countsTotalEmm)
# print "eProb in ins state:\n",eProbX
return tProbHmm, eProbM, eProbX
