Source code for p4.constraints

import p4.func
from p4.p4exceptions import P4Error

[docs]class Constraints(object): """A container for tree topology constraints. taxNames A list of taxNames in the same order as in the data or alignment, and the same order as in other tree or trees objects. constraintTree A partially resolved tree object that describes the constraints. You need to include all the taxNames. For example:: tNames = ['A', 'B', 'C', 'D', 'E'] read('(A, B, (E, D), C);') constTree = var.trees.pop() c = Constraints(tNames, constTree) t = p4.func.randomTree(taxNames=tName, constraints=c) You can pass a Constraints object to p4.func.randomTree() and Mcmc() to enforce constraints. """ def __init__(self, taxNames, constraintTree): self.tree = constraintTree self.tree.taxNames = taxNames self.allOnes = 2 ** (self.tree.nTax) - 1 self.tree.makeSplitKeys() self.constraints = [] #self.tree.draw() for n in self.tree.iterInternalsNoRoot(): = if not in self.constraints: self.constraints.append( assert self.constraints, "No constraints?"
[docs] def dump(self): print('Constraints.dump()') print('taxNames:') for i in range(self.tree.nTax): print(' %3i %s' % (i, self.tree.taxNames[i])) print('constraints:') for i in self.constraints: print(p4.func.getSplitStringFromKey(i, self.tree.nTax), i) self.tree.draw()