> An alternate approach, which BioJava *will* help you with, is > to calculate both the forward and the backward DP matrices, > then multiply these together and normalize by the overall > backwards/forwards probability. This then tells you the
By normalize do you mean divide each value by the total forward or backward probability? So by doing this I would expect that the forward-backward prob should equal the forward and the backward probs? Also, can someone enlighten me how the matrices are indexed (there is not much javadoc in DP)? Currently I'm assuming that the x axis is the array returned by getStates and the y axis is the aligned SymbolList from that state path, with a magical state at each end but I'm not too clear on this. All these questions are leading up to the development of some semi markov models or emissions with duration. Also should this be on biojava-dev or are others finding this useful? - Mark ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
