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/***************************************************************************
* PHAST: PHylogenetic Analysis with Space/Time models
* Copyright (c) 2002-2005 University of California, 2006-2010 Cornell
* University. All rights reserved.
*
* This source code is distributed under a BSD-style license. See the
* file LICENSE.txt for details.
***************************************************************************/
#ifndef PUZ_H
#define PUZ_H
#include <category_map.h>
#include <hmm.h>
#include <tree_model.h>
#include <lists.h>
typedef struct {
CategoryMap *cm; /* category map */
HMM *hmm; /* final HMM, after reflection and
allowance for rate categories */
HMM *functional_hmm, *autocorr_hmm;
/* original HMMs used to create cross
product (NULL if no rate
categories) */
TreeModel **mods; /* array of tree models, after
allowance for rate categories */
int nmods; /* number of tree models (length of
array mods) */
int *state_to_mod; /* mapping of HMM state number to tree
model number */
int *state_to_cat; /* mapping of HMM state number to (spooled)
category number */
int *reverse_compl; /* array of length hmm->nstates
with value 1 for each state
that corresponds to the reverse
strand and value 0 otherwise */
List **cat_to_states; /* one to many mapping */
int *state_to_pattern; /* gap pattern associated with each
state, when modeling indels (-1 for
no gap pattern) */
int nratecats;
} PhyloHMM_Puzzler;
PhyloHMM_Puzzler *puz_new(CategoryMap *cm, TreeModel **tree_models, HMM *hmm,
int reflect_hmm, List *pivot_cats, int nratecats,
double *scaling_consts, double lambda,
List *indel_cats, int nseqs);
void puz_reflect_hmm(PhyloHMM_Puzzler *puz, List *pivot_cats);
void puz_create_autocorr_hmm(HMM *hmm, double lambda);
void puz_rate_cats(PhyloHMM_Puzzler *puz, double *scaling_consts,
double lambda);
void puz_update_cross_prod(PhyloHMM_Puzzler *puz, double lambda);
void puz_free(PhyloHMM_Puzzler *puz);
#endif
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