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/* RogueNaRok is an algorithm for the identification of rogue taxa in a set of phylogenetic trees.
*
* Moreover, the program collection comes with efficient implementations of
* * the unrooted leaf stability by Thorley and Wilkinson
* * the taxonomic instability index by Maddinson and Maddison
* * a maximum agreement subtree implementation (MAST) for unrooted trees
* * a tool for pruning taxa from a tree collection.
*
* Copyright October 2011 by Andre J. Aberer
*
* Tree I/O and parallel framework are derived from RAxML by Alexandros Stamatakis.
*
* This program is free software; you may redistribute it and/or
* modify its 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.
*
* For any other inquiries send an Email to Andre J. Aberer
* andre.aberer at googlemail.com
*
* When publishing work that is based on the results from RogueNaRok, please cite:
* Andre J. Aberer, Denis Krompaß, Alexandros Stamatakis. RogueNaRok: an Efficient and Exact Algorithm for Rogue Taxon Identification. (unpublished) 2011.
*
*/
#ifndef BITVECTOR_H
#define BITVECTOR_H
#include <stdlib.h>
#include <assert.h>
#include <string.h>
#include "common.h"
typedef unsigned int BitVector;
#define BIT_COUNT(x) precomputed16_bitcount(x)
#define NUMBER_BITS_IN_COMPLEMENT(bipartition) (mxtips - dropRound - bipartition->numberOfBitsSet)
#define GET_BITVECTOR_LENGTH(x) (((x) % MASK_LENGTH) ? ((x) / MASK_LENGTH + 1) : ((x) / MASK_LENGTH))
#define FLIP_NTH_BIT(bitVector,n) (bitVector[(n) / MASK_LENGTH] |= mask32[ (n) % MASK_LENGTH ])
#define UNFLIP_NTH_BIT(bitVector,n) (bitVector[(n) / MASK_LENGTH] &= ~mask32[ (n) % MASK_LENGTH ])
#define NTH_BIT_IS_SET(bitVector,n) (bitVector[(n) / MASK_LENGTH] & mask32[(n) % MASK_LENGTH])
#define NTH_BIT_IS_SET_IN_INT(integer,n) (integer & mask32[n])
#define MASK_LENGTH 32
__attribute__((__common__)) char bits_in_16bits [0x1u << 16];
extern BitVector *mask32;
void initializeMask();
BitVector genericBitCount(BitVector* bitVector, int bitVectorLength);
BitVector precomputed16_bitcount (BitVector n);
void compute_bits_in_16bits(void);
void printBitVector(BitVector *bv, int length);
void freeBitVectors(BitVector **v, int n);
BitVector *copyBitVector(BitVector *bitVector, int bitVectorLength);
void printBitVector(BitVector *bv, int length);
#endif
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