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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 (unpublished) 2011.
*
*/
#include "BitVector.h"
BitVector *mask32;
void initializeMask()
{
int i;
mask32 = CALLOC(MASK_LENGTH, sizeof(BitVector));
mask32[0] = 1;
for(i = 1; i < MASK_LENGTH; ++i)
mask32[i] = mask32[i-1] << 1;
}
void printBitVector(BitVector *bv, int length)
{
int i ;
for(i = 0; i < length * 32; ++i)
printf("%d", NTH_BIT_IS_SET(bv, i) ? 1 : 0);
}
void freeBitVectors(unsigned int **v, int n)
{
int i;
for(i = 1; i < n; i++)
free(v[i]);
}
boolean areSameBitVectors(BitVector *a, BitVector *b, int bitVectorLength)
{
int
i;
FOR_0_LIMIT(i,bitVectorLength)
if(a[i] != b[i])
return FALSE;
return TRUE;
}
BitVector genericBitCount(BitVector* bitVector, int bitVectorLength)
{
BitVector
i,
result = 0;
for(i = 0; i < bitVectorLength; i++)
result += BIT_COUNT(bitVector[i]);
return result;
}
static int iterated_bitcount(BitVector n)
{
int
count=0;
while(n)
{
count += n & 0x1u ;
n >>= 1 ;
}
return count;
}
void compute_bits_in_16bits(void)
{
BitVector i;
for (i = 0; i < (0x1u<<16); i++)
bits_in_16bits[i] = iterated_bitcount(i);
return ;
}
BitVector precomputed16_bitcount (BitVector n)
{
/* works only for 32-bit int*/
return bits_in_16bits [n & 0xffffu]
+ bits_in_16bits [(n >> 16) & 0xffffu] ;
}
BitVector *copyBitVector(BitVector *bitVector, int bitVectorLength)
{
BitVector *result = CALLOC(bitVectorLength, sizeof(BitVector));
memcpy(result, bitVector,bitVectorLength * sizeof(BitVector));
return result;
}
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