ξ Ec@sddZddlZddlZddlZddlmZdfdYZdfdYZdS(s,Deal with representations of Markov Models. iN(t MutableSeqtMarkovModelBuildercBseZdZdZdZdZdZdZdZdZ dZ ddd Z d Z d Zd Zd ZdZRS(siInterface to build up a Markov Model. This class is designed to try to separate the task of specifying the Markov Model from the actual model itself. This is in hopes of making the actual Markov Model classes smaller. So, this builder class should be used to create Markov models instead of trying to initiate a Markov Model directly. icCsR||_||_i|_|j|||_i|_|j|||_dS(s;Initialize a builder to create Markov Models. Arguments: o state_alphabet -- An alphabet containing all of the letters that can appear in the states o emission_alphabet -- An alphabet containing all of the letters for states that can be emitted by the HMM. N(t_state_alphabett_emission_alphabetttransition_probt _all_blankt emission_probttransition_pseudot _all_pseudotemission_pseudo(tselftstate_alphabettemission_alphabet((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/HMM/MarkovModel.pyt__init__s       cCsBi}x5|jD]*}x!|jD]}d|||f