#ifndef _HMM_h_
#define _HMM_h_
/* HMM.h
 *
 * Copyright (C) 2010-2011, 2015 David Weenink
 *
 * This program 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 2 of the License, or (at
 * your option) any later version.
 *
 * This program 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, write to the Free Software
 * Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 */

#include "Strings_extensions.h"
#include "TableOfReal.h"
#include "Collection.h"
#include "GaussianMixture.h"
#include "SSCP.h"
#include "Index.h"

#include "HMM_def.h"
oo_CLASS_CREATE (HMM_State, Daata);
oo_CLASS_CREATE (HMM_Observation, Daata);
oo_CLASS_CREATE (HMM_Viterbi, Daata);
oo_CLASS_CREATE (HMM, Daata);

Thing_define (HMM_BaumWelch, Daata) {
	// new data:
	public:
		long capacity;
		long numberOfTimes;
		long totalNumberOfSequences;
		long numberOfStates;
		long numberOfSymbols;
		double lnProb;
		double minProb;
		double **alpha;
		double **beta;
		double *scale;
		double **gamma;
		double ***xi;
		double **aij_num, **aij_denom;
		double **bik_num, **bik_denom;
	// overridden methods:
		virtual void v_destroy ();
};

Thing_define (HMM_StateSequence, Strings) {
};

Thing_define (HMM_ObservationSequence, Table) {
};
// First column is always a symbol, if only 1 column then symbols only

Thing_define (HMM_ObservationSequences, Collection) {
};

autoHMM_ObservationSequence HMM_ObservationSequence_create (long numberOfItems, long dataLength);

void HMM_ObservationSequence_removeObservation (HMM_ObservationSequence me, long index);

autoStrings HMM_ObservationSequence_to_Strings (HMM_ObservationSequence me);

autoHMM_ObservationSequence Strings_to_HMM_ObservationSequence (Strings me);

autoStringsIndex HMM_ObservationSequence_to_StringsIndex (HMM_ObservationSequence me);

autoStringsIndex HMM_and_HMM_ObservationSequence_to_StringsIndex (HMM me, HMM_ObservationSequence thee);

autoTableOfReal HMM_ObservationSequence_to_TableOfReal_transitions (HMM_ObservationSequence me, int probabilities);

autoTableOfReal HMM_and_HMM_ObservationSequence_to_TableOfReal_transitions (HMM me, HMM_ObservationSequence thee, int probabilities);

autoHMM_ObservationSequences HMM_ObservationSequences_create ();

long HMM_ObservationSequence_getNumberOfObservations (HMM_ObservationSequence me);

long HMM_ObservationSequences_getLongestSequence (HMM_ObservationSequences me);

autoTableOfReal HMM_StateSequence_to_TableOfReal_transitions (HMM_StateSequence me);

autoTableOfReal HMM_and_HMM_StateSequence_to_TableOfReal_transitions (HMM me, HMM_StateSequence thee, int probabilities);

autoHMM_StateSequence HMM_StateSequence_create (long numberOfItems);

autoStrings HMM_StateSequence_to_Strings (HMM_StateSequence me);

void HMM_State_setLabel (HMM_State me, char32 *label);


autoHMM HMM_create (int leftToRight, long numberOfStates, long numberOfObservationSymbols);

autoHMM HMM_createSimple (int leftToRight, const char32 *states_string, const char32 *symbols_string);

autoHMM HMM_createContinuousModel (int leftToRight, long numberOfStates, long numberOfObservationSymbols,
	long numberOfMixtureComponentsPerSymbol, long componentDimension, long componentStorage);

autoHMM HMM_createFullContinuousModel (int leftToRight, long numberOfStates, long numberOfObservationSymbols,
	long numberOfFeatureStreams, long *dimensionOfStream, long *numberOfGaussiansforStream);

autoHMM HMM_createFromHMM_ObservationSequence (HMM_ObservationSequence me, long numberOfStates, int leftToRight);

void HMM_draw (HMM me, Graphics g, int garnish);

void HMM_drawBackwardProbabilitiesIllustration (Graphics g, bool garnish);

void HMM_drawForwardProbabilitiesIllustration (Graphics g, bool garnish);

void HMM_drawForwardAndBackwardProbabilitiesIllustration (Graphics g, bool garnish);

void HMM_addObservation (HMM me, thou);

void HMM_addState (HMM me, thou);

void HMM_setDefaultStates (HMM me);

void HMM_setDefaultObservations (HMM me);

void HMM_setDefaultTransitionProbs (HMM me);

void HMM_setDefaultStartProbs (HMM me);

void HMM_setDefaultEmissionProbs (HMM me);

void HMM_setDefaultMixingProbabilities (HMM me);

void HMM_unExpandPCA (HMM me);
/* Unexpand all the PCA's in the gaussian mixtures */



/*
	Set the probabilities. A probability zero value indicates that this p cannot be changed during training/learning.
*/
void HMM_setTransitionProbabilities (HMM me, long state_number, char32 *state_probs);

void HMM_setEmissionProbabilities (HMM me, long state_number, char32 *emission_probs);

void HMM_setStartProbabilities (HMM me, char32 *probs);


double HMM_getProbabilityAtTimeBeingInState (HMM me, long itime, long istate);

double HMM_getProbabilityAtTimeBeingInStateEmittingSymbol (HMM me, long itime, long istate, long isymbol);

double HMM_getExpectedValueOfDurationInState (HMM me, long istate);

double HMM_getProbabilityOfStayingInState (HMM me, long istate, long numberOfTimeUnits);

double HMM_and_HMM_getCrossEntropy (HMM me, HMM thee, long observationLength, int symmetric);

double HMM_and_HMM_and_HMM_ObservationSequence_getCrossEntropy (HMM me, HMM thee, HMM_ObservationSequence him);

autoTableOfReal HMM_extractTransitionProbabilities (HMM me);

autoTableOfReal HMM_extractEmissionProbabilities (HMM me);

/* HMM & HMM_ObservationSequence ****/

autoHMM_ObservationSequence HMM_to_HMM_ObservationSequence (HMM me, long initialState, long numberOfItems);

autoHMM_StateSequence HMM_and_HMM_ObservationSequence_to_HMM_StateSequence (HMM me, HMM_ObservationSequence thee);

double HMM_and_HMM_StateSequence_getProbability (HMM me, HMM_StateSequence thee);

void HMM_and_HMM_ObservationSequences_learn (HMM me, HMM_ObservationSequences thee, double delta_lnp, double minProb);

void HMM_and_HMM_StateSequence_drawTrellis (HMM me, HMM_StateSequence thee, Graphics g, int connect, int garnish);

double HMM_and_HMM_ObservationSequence_getProbability (HMM me, HMM_ObservationSequence thee);

double HMM_and_HMM_ObservationSequence_getCrossEntropy (HMM me, HMM_ObservationSequence thee);

double HMM_and_HMM_ObservationSequence_getPerplexity (HMM me, HMM_ObservationSequence thee);

// somewhere else
void MelderInfo_lnp (double logp);
autoTableOfReal Strings_to_TableOfReal_transitions (Strings me, int probabilities);

#endif /* _HMM_h_ */
