topology_common.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_topology_common_h_
#define _biomcmc_topology_common_h_

#include "bipartition.h"
#include "distance_matrix.h"
#include "empirical_frequency.h"

typedef struct topol_node_struct* topol_node;
typedef struct topology_struct* topology;

struct topol_node_struct
{
  topol_node up, right, left, sister; 
  int id, level; 
  int mid[5];    
  bool internal, 
       u_done,   
       d_done;   
  bipartition split;    
};

struct topology_struct
{
  topol_node *nodelist; 
  double *blength;      
  int id;               
  topol_node root;      
  int nleaves;          
  int nnodes;           
  topol_node undo_prune;   
  topol_node undo_regraft; 
  bool undo_lca;           
  topol_node *postorder;   
  topol_node *undone;      
  int n_undone;  
  uint32_t hashID1, hashID2; 
  bool traversal_updated;  
  int ref_counter;         
  char_vector taxlabel;    
  int *index;             
  bool quasirandom;        
};


topology new_topology (int nleaves);
void topology_malloc_blength (topology tree);
void del_topology (topology topol);

/* DEBUG function */
void debug_topol (topology tree);

void copy_topology_from_topology (topology to_tree, topology from_tree);

void update_topology_sisters (topology tree);

void update_topology_traversal (topology tree);

bool topology_is_equal (topology t1, topology t2);

bool topology_is_equal_unrooted (topology t1, topology t2, bool use_root_later);

void reorder_topology_leaves (topology tree);

bool node1_is_child_of_node2 (topol_node node1, topol_node node2);

char * topology_to_string_by_id (const topology tree, double *blen);

char * topology_to_string_create_name (const topology tree, double *blen);

char * topology_to_string_by_name (const topology tree, double *blen);

void graphviz_file_topology (FILE * fout, char *label, const topology tree);

void apply_spr_at_nodes (topology p, topol_node prune, topol_node regraft, bool update_done);
void apply_spr_at_nodes_LCAprune (topology tree, topol_node prune, topol_node regraft, bool update_done);
void apply_spr_at_nodes_notLCAprune (topology tree, topol_node prune, topol_node regraft, bool update_done);
void topology_undo_random_move (topology tree, bool update_done);
void clear_topology_flags (topology tree);
void raise_topology_flags (topology tree);
void topology_reset_random_move (topology tree);

int copy_topology_to_intvector_by_postorder (topology tree, int *ivec);
int copy_intvector_to_topology_by_postorder (topology tree, int *ivec);
void copy_topology_to_intvector_by_id (topology tree, int *ivec);
void copy_intvector_to_topology_by_id (topology tree, int *ivec);

#endif