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 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 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
