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/*
* Copyright (C) 2014-2021 Brian L. Browning
*
* This file is part of Beagle
*
* Beagle is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Beagle is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package imp;
/**
* <p>Class {@code StateProbs} stores a subset of Li and Stephens HMM states
* and associated probabilities for a target haplotype.
* </p>
* <p>All instances of interface {@code StateProbs} are required to be
* immutable.
* </p>
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public interface StateProbs {
/**
* Returns the target haplotype index.
* @return the target haplotype index
*/
int targHap();
/**
* Returns the number of target markers.
* @return the number of target markers
*/
int nTargMarkers();
/**
* Returns the number of stored HMM states at the specified
* target marker.
* @param targMarker a target marker index
* @return the number of stored HMM states at the specified target marker
* @throws IndexOutOfBoundsException if
* {@code marker < 0 || marker >= this.nTargMarkers()}
*/
int nStates(int targMarker);
/**
* Returns the specified reference haplotype index.
* @param targMarker a target marker index
* @param index a stored state index at the specified target marker
* @return the specified reference haplotype index
* @throws IndexOutOfBoundsException if
* {@code targMarker < 0 || targMarker >= this.nTargMarkers()}
* @throws IndexOutOfBoundsException if
* {@code index < 0 || index >= this.nStates(targMarker)}
*/
int refHap(int targMarker, int index);
/**
* Returns the probability of the specified state at the specified target
* marker.
* @param targMarker a target marker index
* @param index a stored state index
* @return the probability of the specified state at the specified target
* marker
* @throws IndexOutOfBoundsException if
* {@code targMarker < 0 || targMarker >= this.nTargMarkers()}
* @throws IndexOutOfBoundsException if
* {@code index < 0 || index >= this.nStates(targMarker)}
*/
float probs(int targMarker, int index);
/**
* Returns the probability of the specified state at the marker following
* the specified target marker. If
* {@code (targMarker + 1 == this.nTargMarkers())}, the probability of
* the specified state at the specified target marker is returned.
* @param targMarker a target marker index
* @param index a stored state index
* @return the probability of the specified state at the marker following
* the specified target marker
* @throws IndexOutOfBoundsException if
* {@code targMarker < 0 || targMarker >= this.nTargMarkers()}
* @throws IndexOutOfBoundsException if
* {@code index < 0 || index >= this.nStates(targMarker)}
*/
float probsP1(int targMarker, int index);
}
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