def A(parasiteTree, hostTree, phi, ep, eh):
''' The A table for the dynamic program. '''
global Amemo
if (ep, eh) in Amemo: return Amemo[(ep, eh)]
if tipEdge(eh, hostTree):
if tipEdge(ep, parasiteTree) and \
phi[endVertex(ep, parasiteTree)] == endVertex(eh, hostTree):
return [CostVector(0, 0, 0, 0, 1)]
else:
return [CostVector(INF, INF, INF, INF, 0)]
else:
ehLeftChild = leftChildEdge(eh, hostTree)
ehRightChild = rightChildEdge(eh, hostTree)
# Cospeciation
if tipEdge(ep, parasiteTree):
cospeciation = [CostVector(INF, INF, INF, INF, 0)]
else:
epLeftChild = leftChildEdge(ep, parasiteTree)
epRightChild = rightChildEdge(ep, parasiteTree)
cospeciation1 = merge(C(parasiteTree, hostTree, phi, \
epLeftChild, ehLeftChild), \
C(parasiteTree, hostTree, phi, \
epRightChild, ehRightChild), \
ep, eh, epLeftChild, ehLeftChild, \
epRightChild, ehRightChild, "cospeciation")
cospeciation2 = merge(C(parasiteTree, hostTree, phi, \
epLeftChild, ehRightChild), \
C(parasiteTree, hostTree, phi, \
epRightChild, ehLeftChild), \
ep, eh, epLeftChild, ehRightChild, \
epRightChild, ehLeftChild, "cospeciation")
cospeciation = cospeciation1 + cospeciation2
# Loss
loss1 = lossmerge(ep, eh, ehLeftChild, \
C(parasiteTree, hostTree, phi, ep, ehLeftChild))
loss2 = lossmerge(ep, eh, ehRightChild, \
C(parasiteTree, hostTree, phi, ep, ehRightChild))
loss = loss1 + loss2
output = paretoFilter(cospeciation + loss)
Amemo[(ep, eh)] = output
return output
def merge(CVlist1, CVlist2, ep, eh, epChild1, ehChild1, epChild2, \
ehChild2, eventType):
''' Given two lists of CostVectors, returns a new list of CostVectors, each
of which is the sum of a pair of vectors from the two given lists.'''
global CVevents
global CVallEvents
global CandidateCVlist
intersection = CONFIG.intersection
if intersection:
global CVseen
global CVcommonEvents
output = []
for v in CVlist1:
for w in CVlist2:
if eventType == "cospeciation":
newCV = CostVector(1, 0, 0, 0, 1) + v + w
elif eventType == "duplication":
newCV = CostVector(0, 1, 0, 0, 1) + v + w
else: # eventType == "switch":
newCV = CostVector(0, 0, 1, 0, 1) + v + w
keepnewCV = True
for cv in CandidateCVlist:
if cv < newCV:
keepnewCV = False
break
if keepnewCV:
output.append(newCV)
vsoln = (epChild1, ehChild1) + v.toTupleCDSL()
wsoln = (epChild2, ehChild2) + w.toTupleCDSL()
if eventType == "switch":
eventType = "switch to " + str(ehChild2)
nswe = (ep, eh, eventType) + newCV.toTupleCDSL()
ns = (ep, eh) + newCV.toTupleCDSL()
CVevents[nswe].add(nswe)
CVevents[nswe] = CVevents[nswe].\
union(CVallEvents[vsoln]).\
union(CVallEvents[wsoln])
CVallEvents[ns] = CVallEvents[ns].union(CVevents[nswe])
if intersection:
key = newCV.toTupleCDSL()
if CVseen[key]:
CVcommonEvents[key] = CVcommonEvents[key].\
intersection(CVevents[nswe])
else:
CVcommonEvents[key] = CVevents[nswe]
CVseen[key] = True
return output
def C(parasiteTree, hostTree, phi, ep, eh):
''' The C table for the dynamic program. '''
global Cmemo
if (ep, eh) in Cmemo: return Cmemo[(ep, eh)]
# Option 1: Pass through
passThrough = A(parasiteTree, hostTree, phi, ep, eh)
if tipEdge(ep, parasiteTree): # The options below don't apply to tips
return passThrough
else:
epLeftChild = leftChildEdge(ep, parasiteTree)
epRightChild = rightChildEdge(ep, parasiteTree)
# Option 2: Duplicate here
duplicate = CostVector(0, 1, 0, 0, 1) * \
merge(C(parasiteTree, hostTree, phi, epLeftChild, eh), \
C(parasiteTree, hostTree, phi, epRightChild, eh))
# Option 3: Switch here
switch1 = CostVector(0, 0, 1, 0, 1) * \
merge(C(parasiteTree, hostTree, phi, epLeftChild, eh), \
switches(parasiteTree, hostTree, phi, epRightChild, eh))
switch2 = CostVector(0, 0, 1, 0, 1) * \
merge(C(parasiteTree, hostTree, phi, epRightChild, eh), \
switches(parasiteTree, hostTree, phi, epLeftChild, eh))
switch = switch1 + switch2
output = paretoFilter(passThrough + duplicate + switch)
Cmemo[(ep, eh)] = output
return output
def lossmerge(ep, eh, ehChild, CVlist):
global CVevents
global CVallEvents
global CandidateCVlist
intersection = CONFIG.intersection
if intersection:
global CVseen
global CVcommonEvents
output = []
for v in CVlist:
newCV = CostVector(0, 0, 0, 1, 1) + v
keepnewCV = True
for cv in CandidateCVlist:
if cv < newCV:
keepnewCV = False
break
if keepnewCV:
output.append(newCV)
vsoln = (ep, ehChild) + v.toTupleCDSL()
nswe = (ep, eh, "loss " + str(ehChild)) + newCV.toTupleCDSL()
ns = (ep, eh) + newCV.toTupleCDSL()
CVevents[nswe].add(nswe)
CVevents[nswe] = CVevents[nswe].union(CVallEvents[vsoln])
CVallEvents[ns] = CVallEvents[ns].union(CVevents[nswe])
if intersection:
key = newCV.toTupleCDSL()
if CVseen[key]:
CVcommonEvents[key] = CVcommonEvents[key].\
intersection(CVevents[nswe])
else:
CVcommonEvents[key] = CVevents[nswe]
CVseen[key] = True
return output
def lossmerge(ep, eh, ehChild, CVlist):
global CVevents
global CVallEvents
global CandidateCVlist
intersection = CONFIG.intersection
if intersection:
global CVseen
global CVcommonEvents
output = []
for v in CVlist:
newCV = CostVector(0, 0, 0, 1, 1) + v
keepnewCV = True
for cv in CandidateCVlist:
if cv < newCV:
keepnewCV = False
break
if keepnewCV:
output.append(newCV)
vsoln = (ep, ehChild) + v.toTupleCDSL()
nswe = (ep, eh, "loss "+str(ehChild)) + newCV.toTupleCDSL()
ns = (ep, eh) + newCV.toTupleCDSL()
CVevents[nswe].add(nswe)
CVevents[nswe] = CVevents[nswe].union(CVallEvents[vsoln])
CVallEvents[ns] = CVallEvents[ns].union(CVevents[nswe])
if intersection:
key = newCV.toTupleCDSL()
if CVseen[key]:
CVcommonEvents[key] = CVcommonEvents[key].\
intersection(CVevents[nswe])
else:
CVcommonEvents[key] = CVevents[nswe]
CVseen[key] = True
return output
def merge(CVlist1, CVlist2, ep, eh, epChild1, ehChild1, epChild2, \
ehChild2, eventType):
''' Given two lists of CostVectors, returns a new list of CostVectors, each
of which is the sum of a pair of vectors from the two given lists.'''
global CVevents
global CVallEvents
global CandidateCVlist
intersection = CONFIG.intersection
if intersection:
global CVseen
global CVcommonEvents
output = []
for v in CVlist1:
for w in CVlist2:
if eventType == "cospeciation":
newCV = CostVector(1, 0, 0, 0, 1) + v + w
elif eventType == "duplication":
newCV = CostVector(0, 1, 0, 0, 1) + v + w
else: # eventType == "switch":
newCV = CostVector(0, 0, 1, 0, 1) + v + w
keepnewCV = True
for cv in CandidateCVlist:
if cv < newCV:
keepnewCV = False
break
if keepnewCV:
output.append(newCV)
vsoln = (epChild1, ehChild1) + v.toTupleCDSL()
wsoln = (epChild2, ehChild2) + w.toTupleCDSL()
if eventType == "switch": eventType = "switch to "+str(ehChild2)
nswe = (ep, eh, eventType) + newCV.toTupleCDSL()
ns = (ep, eh) + newCV.toTupleCDSL()
CVevents[nswe].add(nswe)
CVevents[nswe] = CVevents[nswe].\
union(CVallEvents[vsoln]).\
union(CVallEvents[wsoln])
CVallEvents[ns] = CVallEvents[ns].union(CVevents[nswe])
if intersection:
key = newCV.toTupleCDSL()
if CVseen[key]:
CVcommonEvents[key] = CVcommonEvents[key].\
intersection(CVevents[nswe])
else:
CVcommonEvents[key] = CVevents[nswe]
CVseen[key] = True
return output
def tupleToCV(entry):
return CostVector(entry[0], entry[1], entry[2], entry[3], entry[4])