Package org.biojava.bio.dp

Interface EmissionState

    • Field Detail

      • DISTRIBUTION

        static final ChangeType DISTRIBUTION

        This signals that the distribution associate with an EmissionState has been altered.

        If the distribution has changed its weights, then the event'e getChainedEvent method will return the event fired by the distribution. If one distribution has been replaced by another, then the new and old Distributions will be in current and previous, respectively.

      • ADVANCE

        static final ChangeType ADVANCE

        This signals that the advance array has been altered.

        current and previous should hold the current and previous advances, respectively.

    • Method Detail

      • getAdvance

        int[] getAdvance()
        Determine the number of symbols this state advances along one or more symbol lists. In the simple case, this method should almost always return {1} if it is a true `emmision' state, or {0} if it is a dot state which only emits a gap character. For pairwise HMMs, it will normally return {1, 1} for match state, and {0, 1} or {1, 0} for a gap state. Under some circumstances it may be valid to return values other than 1 or 0, but you should consider the consequences for HMM architecture very carefully, and contact the authors. Developers may wish to return a copy of some underlying array from this method as code outside could modify the array you give

      • setAdvance

        void setAdvance​(int[] advance)
         throws ChangeVetoException
        Set the advance array.
        Parameters:
        advance - an array of ints, specifying how many symbols are consumed from each sequence
        Throws:
        ChangeVetoException - if the implementation doesn't support setting advance, or if the change is vetoed

      • getDistribution

        Distribution getDistribution()

        Get the Distribution associated with this state.

        If the state is to be added to an HMM, then the state's emission spectrum must be compatible with the HMM - that is, their emission alphabets must match.

        Returns:
        the current Distribution object used by this state