#NEWLINE# def initializeQMatrix( codons ) : #NEWLINE# #INDENT# 'get an initialized Q matrix.' #NEWLINE# Q = { #NEWLINE# #INDENT# #NEWLINE# #UNINDENT# } #NEWLINE# for codon_i in codons : #NEWLINE# #INDENT# Q [ codon_j ] = { #NEWLINE# #INDENT# #NEWLINE# #UNINDENT# } #NEWLINE# for codon_j in codons : #NEWLINE# #INDENT# Q [ codon_i ] [ codon_j ] = 0.0 #NEWLINE# #UNINDENT# #UNINDENT# return Q