def calc_NJ_trees(self, verbosity=0):
self.analysis = 'nj'
for rec in self.records:
runPhyml(rec, analysis='nj', verbosity=verbosity,
tmpdir=self.tmpdir)
rec.tree = TrClTree.cast(rec.tree)
if verbosity == 1:
print
def calc_NJ_trees(self, analysis='nj', verbosity=0):
self.analysis = analysis
for rec in self.records:
runPhyml(rec, self.tmpdir, analysis=analysis, verbosity=verbosity,
taxon_set=self.taxon_set)
rec.tree = TrClTree.cast(rec.tree)
if verbosity == 1:
print
def calc_ML_trees(self, verbosity=0):
self.analysis = 'ml'
for rec in self.records:
runPhyml(rec,
analysis=self.analysis,
verbosity=verbosity,
tmpdir=self.tmpdir)
rec.tree = TrClTree.cast(rec.tree)
def calc_NJ_trees(self, verbosity=0):
self.analysis = 'nj'
for rec in self.records:
runPhyml(rec,
analysis='nj',
verbosity=verbosity,
tmpdir=self.tmpdir)
rec.tree = TrClTree.cast(rec.tree)
if verbosity == 1:
print
def add(self, index_list):
""" Takes a tuple of indices. Concatenates the records in the record
list at these indices, and builds a tree. Returns the tree """
if index_list in self.concats:
return self.concats[index_list]
concat = self.concatenate(index_list)
if self.analysis == 'TreeCollection':
guidetrees = [self.records[n].tree
for n in index_list][:self.max_guidetrees]
tree = TrClTree.cast(
runTC(concat, guidetrees, verbosity=self.verbosity))
else:
tree = TrClTree.cast(
runPhyml(concat,
analysis=self.analysis,
verbosity=self.verbosity))
# concat local variable dies here and goes to garbage collect
self.concats[index_list] = tree
return tree
def add(self, index_list):
""" Takes a tuple of indices. Concatenates the records in the record
list at these indices, and builds a tree. Returns the tree """
if index_list in self.concats:
return self.concats[index_list]
concat = self.concatenate(index_list)
if self.analysis == 'TreeCollection':
guidetrees = [self.records[n].tree for n in
index_list][:self.max_guidetrees]
tree = TrClTree.cast(runTC(concat, guidetrees,
verbosity=self.verbosity))
else:
tree = TrClTree.cast(runPhyml(concat, analysis=self.analysis,
verbosity=self.verbosity))
# concat local variable dies here and goes to garbage collect
self.concats[index_list] = tree
return tree
def calc_ML_trees(self, verbosity=0):
self.analysis = 'ml'
for rec in self.records:
runPhyml(rec, analysis=self.analysis, verbosity=verbosity,
tmpdir=self.tmpdir)
rec.tree = TrClTree.cast(rec.tree)