bipartition.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_bipartition_h_
#define _biomcmc_bipartition_h_


#include "lowlevel.h" 

typedef struct bipartition_struct* bipartition;
typedef struct bipsize_struct* bipsize;
typedef bipartition* tripartition; /* just a vector of size 3 */

struct bipartition_struct 
{
  uint64_t *bs;
  int n_ones;
  bipsize n;
  int ref_counter;
};

struct bipsize_struct
{
  uint64_t mask;
  int ints, bits, original_size;
  int ref_counter;
};

bipartition new_bipartition (int size);
bipsize new_bipsize (int size);
bipartition new_bipartition_copy_from (const bipartition from);
bipartition new_bipartition_from_bipsize (bipsize n);
void del_bipartition (bipartition bip);
void del_bipsize (bipsize n);
void bipsize_resize (bipsize n, int nbits);
void bipartition_initialize (bipartition bip, int position);
void bipartition_zero (bipartition bip);
void bipartition_set (bipartition bip, int position);
void bipartition_set_lowlevel (bipartition bip, int i, int j);
void bipartition_unset (bipartition bip, int position);
void bipartition_unset_lowlevel (bipartition bip, int i, int j);
void bipartition_copy (bipartition to, const bipartition from);
void bipartition_OR (bipartition result, const bipartition b1, const bipartition b2, bool update_count);
void bipartition_AND (bipartition result, const bipartition b1, const bipartition b2, bool update_count);
void bipartition_ANDNOT (bipartition result, const bipartition b1, const bipartition b2, bool update_count);
void bipartition_XOR (bipartition result, const bipartition b1, const bipartition b2, bool update_count);
void bipartition_XORNOT (bipartition result, const bipartition b1, const bipartition b2, bool update_count);
void bipartition_NOT (bipartition result, const bipartition bip);
void bipartition_count_n_ones (const bipartition bip);
void bipartition_to_int_vector (const bipartition b, int *id, int vecsize);
bool bipartition_is_equal (const bipartition b1, const bipartition b2);
bool bipartition_is_equal_bothsides (const bipartition b1, const bipartition b2);
int compare_bipartitions_increasing (const void *a1, const void *a2);
int compare_bipartitions_decreasing (const void *a1, const void *a2);
bool bipartition_is_larger (const bipartition b1, const bipartition b2);
void bipartition_flip_to_smaller_set (bipartition bip);
bool bipartition_is_bit_set (const bipartition bip, int position);
bool bipartition_contains_bits (const bipartition b1, const bipartition b2);
void bipartition_print_to_stdout (const bipartition b1);
void bipartition_replace_bit_in_vector (bipartition *bvec, int n_b, int to, int from, bool reduce);
void bipartition_resize_vector (bipartition *bvec, int n_b);

tripartition new_tripartition (int nleaves);
void del_tripartition (tripartition trip);
void store_tripartition_from_bipartitions (tripartition tri, bipartition b1, bipartition b2);
void sort_tripartition (tripartition tri);
int align_tripartitions (tripartition tp1, tripartition tp2, hungarian h);
bool tripartition_is_equal (tripartition tp1, tripartition tp2);


#endif