genetree.h

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/* 
 * This file is part of biomcmc-lib, a low-level library for phylogenomic analysis.
 * Copyright (C) 2019-today  Leonardo de Oliveira Martins [ leomrtns at gmail.com;  http://www.leomartins.org ]
 *
 * biomcmc 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 (file "COPYING" or http://www.gnu.org/copyleft/gpl.html).
 */

#ifndef _biomcmc_genetree_h_
#define _biomcmc_genetree_h_

#include "upgma.h"

typedef struct genetree_struct* genetree;
typedef struct speciestree_struct* speciestree;
typedef struct reconciliation_struct* reconciliation;
typedef struct splitset_struct* splitset;

struct genetree_struct
{
  topology t;
  reconciliation rec;
  speciestree sptre;  
  splitset split;
  int *distance, *minmax;
  int ref_counter;
};

struct speciestree_struct
{
  topology t;
  topol_node *mrca; 
  int *spnames_order; 
  int ref_counter;
};

struct reconciliation_struct
{
  topol_node *map_d; 
  topol_node *map_u; 
  int *sp_id,    
      *sp_count, 
      sp_size,   
      size_diff, 
      *dup,      
      *ndup_d,   
      *ndup_u,   
      *nlos_d,   
      *nlos_u,   
      ndups,     
      nloss,     
      ndcos;     
};

struct splitset_struct
{
  int size, spsize, spr, spr_extra, rf, hdist, hdist_reduced; 
  int n_g, n_s, n_agree, n_disagree;
  bipartition *g_split, *s_split, *agree, *disagree, *sp0; /* sp0 points to vec[0], s_split points to vec[x] */
  bipartition prune;
  hungarian h; /* hungarian method for solving the assignment between edges */
  bool match;  
};

// convenience function
genetree new_genetree_speciestree_pair (topology gene, topology species);
genetree new_genetree (topology gene, speciestree sptre);
void del_genetree (genetree gtre);
speciestree new_speciestree (topology species, int *order_of_species_names);
void del_speciestree (speciestree sptre);
void genetree_speciestree_distances (genetree gtre, speciestree sptre);
int count_species_in_index_species_gene (int *sp_id, int max_sp, int n_sp_id);

void genetree_reconcile_speciestree (genetree gtre, speciestree sptre);
void genetree_dSPR_speciestree (genetree gtre, speciestree sptre, int level);

#endif