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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.
***************************************************************************/
/* $Id: phylo_fit.h,v 1.17 2008-11-12 02:07:59 acs Exp $ */
#ifndef PHYLO_FIT_H
#define PHYLO_FIT_H
/* default minimum number of informative sites (see -I) */
#define DEFAULT_NSITES_THRESHOLD 50
/* default starting alpha for dgamma */
#define DEFAULT_ALPHA 1
#include <tree_model.h>
#include <msa.h>
#include <category_map.h>
#include <stringsplus.h>
#include <lists.h>
#include <gff.h>
#include <list_of_lists.h>
struct phyloFit_struct {
MSA *msa;
char *output_fname_root,
*reverse_group_tag,
*root_seqname, *subtree_name, *error_fname,
*see_for_help, *parsimony_cost_fname,
*msa_fname; //note: msa_fname will not be read by run_phyloFit.
//The msa should already be loaded. msa_fname can be
//optionally set for producing informative messages
int subst_mod, quiet, nratecats, use_em,
window_size, window_shift, use_conditionals,
precision, likelihood_only, do_bases,
do_expected_nsubst, do_expected_nsubst_tot,
do_expected_nsubst_col,
random_init, estimate_backgd, estimate_scale_only,
do_column_probs, nonoverlapping, gaps_as_bases,
no_freqs, no_rates, assume_clock,
init_parsimony, parsimony_only, no_branchlens,
label_categories, symfreq, init_backgd_from_data,
use_selection, max_em_its;
unsigned int nsites_threshold;
TreeNode *tree;
CategoryMap *cm;
String *nooptstr;
List *cats_to_do_str, *window_coords,
*ignore_branches, *alt_mod_str,
*bound_arg, *rate_consts,
*label_str, *label_type;
double alpha, selection;
GFF_Set *gff;
TreeModel *input_mod;
FILE *logf;
//results go here if not-null
ListOfLists *results;
};
struct phyloFit_struct* phyloFit_struct_new();
int run_phyloFit(struct phyloFit_struct *pf);
void print_post_prob_stats(TreeModel *mod, MSA *msa, char *output_fname_root,
int do_bases, int do_expected_nsubst,
int do_expected_nsubst_tot,
int do_expected_nsubst_col,
int do_every_site,
int cat, int quiet,
ListOfLists *results);
#define BRANCH_TYPE 0
#define SUBTREE_TYPE 1
#endif
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