def __init__(self):
AbstractAlgorithm.__init__(self)
self.place_nomatch_fragments = False
''' Hardcoded E-Lim for hmmsearch ''' #TODO: what to do with this
self.elim = 99999999
self.filters = False
self.strategy = options().exhaustive.strategy
self.minsubsetsize = int(options().exhaustive.minsubsetsize)
#Temp fix for now,
self.molecule = self.options.molecule
def __init__(self):
AbstractAlgorithm.__init__(self)
self.place_nomatch_fragments = False
''' Hardcoded E-Lim for hmmsearch ''' #TODO: what to do with this
self.elim = 99999999
self.filters = False
self.strategy = options().exhaustive.strategy
self.minsubsetsize = int(options().exhaustive.minsubsetsize)
#Temp fix for now,
self.molecule = self.options.molecule
def read_alignment_and_tree(self):
(alignment, tree) = AbstractAlgorithm.read_alignment_and_tree(self)
# TODO: Check for rooted input
# if not tree.is_rooted:
# raise Exception ("For TIPP, backbone tree should be correctly
# rooted according to the taxonomy.")
return (alignment, tree)
def read_alignment_and_tree(self):
(alignment, tree) = AbstractAlgorithm.read_alignment_and_tree(self)
# TODO: Check for rooted input
# if not tree.is_rooted:
# raise Exception ("For TIPP, backbone tree should be correctly
# rooted according to the taxonomy.")
return (alignment, tree)
def check_options(self, supply=[]):
if (options().info_file is None):
supply = supply + ["raxml file"]
AbstractAlgorithm.check_options(self, supply)
def check_options(self, supply = []):
AbstractAlgorithm.check_options(self,supply)
def check_options(self, supply = []):
AbstractAlgorithm.check_options(self,supply)
def check_options(self, supply=[]):
if (options().info_file is None):
supply = supply + ["raxml file"]
AbstractAlgorithm.check_options(self, supply)
