def _commonCStuff(self, resetEmpiricalComps=True):
"""Allocate and set c-stuff, and setPrams."""
if not self.data:
if self.name:
gm = ["Tree %s (_commonCStuff)" % self.name]
else:
gm = ["Tree (_commonCStuff)"]
gm.append(
"This tree has no data attached. Before doing an optimization, likelihood")
gm.append(
"calculation, or simulation, you need to do something like this:")
gm.append(" theTree.data = theData")
raise P4Error(gm)
# print "self.cTree = %s" % self.cTree
if not self.cTree:
# This calls self.modelSanityCheck(), which calls
# self.setEmpiricalComps()
self._allocCStuff(resetEmpiricalComps=resetEmpiricalComps)
# print "About to self.model.setCStuff()"
self.model.setCStuff()
# print "About to self.setCStuff()"
self.setCStuff()
# print "about to p4_setPrams()..."
pf.p4_setPrams(self.cTree, -1) # "-1" means do all parts
def optTest(self):
self._commonCStuff()
theStartTime = time.clock()
doXfer = 0
for i in range(1):
if doXfer:
self.model.setCStuff()
self.setCStuff()
pf.p4_setPrams(self.cTree, -1)
self.logLike = pf.p4_treeLogLike(self.cTree, 0)
if doXfer:
# get the brLens
brLens = pf.p4_getBrLens(self.cTree)
for i in range(len(self.nodes)):
n = self.nodes[i]
if n != self.root:
n.br.len = brLens[i]
# get the other free prams
prams = pf.p4_getFreePrams(self.cTree)
self.model.restoreFreePrams(prams)
print("time %s seconds." % (time.clock() - theStartTime))