Why is the input of the 'hmmgenerate.m' function (emissions) required to have the same number of rows as the transition matrix?

I am trying to generate sequences and states given a set of data, specifying 2 chains (ON or OFF). I am using the 'hmm.m' algorithm posted at Dr Ghahramani's page: http://mlg.eng.cam.ac.uk/zoubin/software.html The output from the 'hmm.m' is a P (emissions matrix) which is a 1x2 and Pi (transition matrix) which is a 2x2. However,the 'hmmgenerate.m' requires that both the emissions and transition have the same number of rows.