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src/c/o/cogent-1.5.3/cogent/evolve/substitution_model.py   cogent(Download)
    def getPredefinedPredicates(self):
        # overridden in subclasses
        return {'indel': predicate.parse('-/?')}
 
    def getPredefinedPredicate(self, name):
    def adaptPredicate(self, pred, label=None):
        if isinstance(pred, str):
            pred = predicate.parse(pred)
        elif callable(pred):
            pred = predicate.UserPredicate(pred)
    def getPredefinedPredicates(self):
        return {
            'transition' : predicate.parse('R/R') | predicate.parse('Y/Y'),
            'transversion' : predicate.parse('R/Y'),
            'indel': predicate.parse('-/?'),

src/p/y/pycogent-HEAD/cogent/evolve/substitution_model.py   pycogent(Download)
    def getPredefinedPredicates(self):
        # overridden in subclasses
        return {'indel': predicate.parse('-/?')}
 
    def getPredefinedPredicate(self, name):
    def adaptPredicate(self, pred, label=None):
        if isinstance(pred, str):
            pred = predicate.parse(pred)
        elif callable(pred):
            pred = predicate.UserPredicate(pred)
    def getPredefinedPredicates(self):
        return {
            'transition' : predicate.parse('R/R') | predicate.parse('Y/Y'),
            'transversion' : predicate.parse('R/Y'),
            'indel': predicate.parse('-/?'),