def __init__(self, abort_event, *args, **kwargs):
MixtureFactory.__init__(self, abort_event, *args, **kwargs)
MultiprocessingBase.__init__(self, abort_event)
self._searcher = SearchEngine(self._abort_event)
self._p_weights = [p.num_components for p in self._primers]
self._pw_sum = sum(self._p_weights)
self._num_p = len(self._primers)
def __init__(self, abort_event, *args, **kwargs):
MixtureFactory.__init__(self, abort_event, *args, **kwargs)
MultiprocessingBase.__init__(self, abort_event)
self._searcher = SearchEngine(self._abort_event)
self._p_weights = [p.num_components for p in self._primers]
self._pw_sum = sum(self._p_weights)
self._num_p = len(self._primers)
def __init__(self, abort_event, reactions, concentrations, precision = 1e-10):
MultiprocessingBase.__init__(self, abort_event)
EquilibriumBase.__init__(self, reactions, concentrations, precision)
#input parameters
self.reactions = reactions
self.concentrations = concentrations
#group reactions by their connected graph components
self._reactions_groups = self._group_reactions()
def __init__(self,
abort_event,
polymerase,
with_exonuclease,
num_cycles,
):
MultiprocessingBase.__init__(self, abort_event)
self._polymerase = polymerase
self._with_exonuclease = with_exonuclease
self._num_cycles = num_cycles
self._PCR_P = deepcopy(tdf.PCR_P)
def __init__(
self,
abort_event,
polymerase,
with_exonuclease,
num_cycles,
):
MultiprocessingBase.__init__(self, abort_event)
self._polymerase = polymerase
self._with_exonuclease = with_exonuclease
self._num_cycles = num_cycles
self._PCR_P = deepcopy(tdf.PCR_P)
def __init__(self,
abort_event,
reactions,
concentrations,
precision=1e-10):
MultiprocessingBase.__init__(self, abort_event)
EquilibriumBase.__init__(self, reactions, concentrations, precision)
#input parameters
self.reactions = reactions
self.concentrations = concentrations
#group reactions by their connected graph components
self._reactions_groups = self._group_reactions()
def __init__(self, abort_event, *args, **kwargs):
iPCR_Interface.__init__(self, abort_event, *args, **kwargs)
MultiprocessingBase.__init__(self, abort_event)
self._blast_results = None
self._bounds = None
self._query = None
#PCR parameters
self._PCR_Simulations = dict()
#query_id use hash of primers instead of all-config hash as in job_id
self._primers_hash = (hash(tuple(self._primers)) & 0xFFFFFFF)
self._query_id = re.split('_[0-9]+\Z', self._job_id)[0]
self._query_id += '_%s' % str(self._primers_hash)
#results
self._results_filename = self._query_id+'-blast.xml'
self._query_filename = self._query_id+'-blast.cfg'
#reports
self._hits_report_filename = '%s-%s-hits.txt' % (self._job_id,
self._PCR_report_suffix.rstrip('-PCR'))
#flags
self._have_blast_results = False
self._have_saved_results = False
def __init__(self, abort_event, job_id, primers):
#initial check
try:
if len(primers) == 0:
raise ValueError('AllSecStructures: no primers given.')
except TypeError:
raise TypeError(('AllSecStructures: primers should be an iterable. '
'Given %s instead') % str(primers))
ReporterInterface.__init__(self)
MultiprocessingBase.__init__(self, abort_event)
#all primers list and concentrations dict
self._primers = primers
self._all_primers = []
self._concentrations = dict()
self._reactions = dict()
self._self = []
self._cross = []
self._all_structures = dict()
self._equilibrium_concentrations = None
#reports
self._job_id = job_id
self._short_structs_filename = job_id+'-structures-short.txt'
self._full_structs_filename = job_id+'-structures-full.txt'
def __init__(self, abort_event, job_id, primers):
#initial check
try:
if len(primers) == 0:
raise ValueError('AllSecStructures: no primers given.')
except TypeError:
raise TypeError(
('AllSecStructures: primers should be an iterable. '
'Given %s instead') % str(primers))
ReporterInterface.__init__(self)
MultiprocessingBase.__init__(self, abort_event)
#all primers list and concentrations dict
self._primers = primers
self._all_primers = []
self._concentrations = dict()
self._reactions = dict()
self._self = []
self._cross = []
self._all_structures = dict()
self._equilibrium_concentrations = None
#reports
self._job_id = job_id
self._short_structs_filename = job_id + '-structures-short.txt'
self._full_structs_filename = job_id + '-structures-full.txt'
def __init__(self, abort_event):
MultiprocessingBase.__init__(self, abort_event)
self._a = 5
def __init__(self, abort_event):
MultiprocessingBase.__init__(self, abort_event)
self._a = 5
