/* * BioJava development code * * This code may be freely distributed and modified under the * terms of the GNU Lesser General Public Licence. This should * be distributed with the code. If you do not have a copy, * see: * * http://www.gnu.org/copyleft/lesser.html * * Copyright for this code is held jointly by the individual * authors. These should be listed in @author doc comments. * * For more information on the BioJava project and its aims, * or to join the biojava-l mailing list, visit the home page * at: * * http://www.biojava.org/ * */ package org.biojava.bio.dp; import org.biojava.bio.symbol.Alignment; /** * Extends the Alignment interface so that it is explicitly used to represent * a state path through an HMM, and the associated emitted sequence and * likelihoods. *
* A state path should have the following structure:
*
* SCORES -> list of step-wise scores for each state (transition + emission)
*
* SEQUENCE -> sequence emitted by the machine
*
* SEQUENCE
* -> Gapped view (gap inserted for every position aligned with a dot-state
* -> Sequence emitted by emission states as Alignment
* label_n = input_SymbolList_n
* -> gapped view of SymbolList_n
*
* I think that this scheme keeps the emitted alignment as close as possible to * a sensible path through the sequence coordinate space, while making this * gappable adapts this to the same co-ordinate system as the HMM state-path * space. *
* * @author Matthew Pocock */ public interface StatePath extends Alignment { /** * Alignment label for the emitted sequence. */ public static final Object SEQUENCE = "SEQUENCE"; /** * Alignment label for the state path. */ public static final Object STATES = "STATES"; /** * Alignment label for the likelyhood at each step. */ public static final Object SCORES = "SCORES"; /** * Return the overall score for this state-path and it's emissions. * * @return the score */ public double getScore(); }