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fastDNAparsimony.c
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fastDNAparsimony.c
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/* RAxML-VI-HPC (version 2.2) a program for sequential and parallel estimation of phylogenetic trees
* Copyright August 2006 by Alexandros Stamatakis
*
* Partially derived from
* fastDNAml, a program for estimation of phylogenetic trees from sequences by Gary J. Olsen
*
* and
*
* Programs of the PHYLIP package by Joe Felsenstein.
*
* 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 enquiries send an Email to Alexandros Stamatakis
* Alexandros.Stamatakis@epfl.ch
*
* When publishing work that is based on the results from RAxML-VI-HPC please cite:
*
* Alexandros Stamatakis:"RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with
* thousands of taxa and mixed models".
* Bioinformatics 2006; doi: 10.1093/bioinformatics/btl446
*/
#ifndef WIN32
#include <sys/times.h>
#include <sys/types.h>
#include <sys/time.h>
#include <unistd.h>
#endif
#include <limits.h>
#include <math.h>
#include <time.h>
#include <stdlib.h>
#include <stdio.h>
#include <ctype.h>
#include <string.h>
#include <stdint.h>
#ifdef __SIM_SSE3
#include <xmmintrin.h>
#include <pmmintrin.h>
#endif
#ifdef __AVX
#include <xmmintrin.h>
#include <immintrin.h>
#endif
#include "axml.h"
extern char run_id[128];
extern char seq_file[1024];
extern char tree_file[1024];
extern char resultFileName[1024];
extern char infoFileName[1024];
extern char randomFileName[1024];
const unsigned int mask32[32] = {1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096, 8192, 16384, 32768, 65536, 131072,
262144, 524288, 1048576, 2097152, 4194304, 8388608, 16777216, 33554432, 67108864, 134217728,
268435456, 536870912, 1073741824, 2147483648U};
/* vector-specific stuff */
#ifdef __SIM_SSE3
#define INTS_PER_VECTOR 4
#define INT_TYPE __m128i
#define CAST __m128i*
#define SET_ALL_BITS_ONE _mm_set_epi32(0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF)
#define VECTOR_LOAD _mm_load_si128
#define VECTOR_BIT_AND _mm_and_si128
#define VECTOR_BIT_OR _mm_or_si128
#define VECTOR_STORE _mm_store_si128
#define VECTOR_AND_NOT _mm_andnot_si128
#define BYTE_ALIGNMENT 16
#endif
#ifdef __AVX
#define INTS_PER_VECTOR 8
#define INT_TYPE __m256d
#define CAST double*
#define SET_ALL_BITS_ONE (__m256d)_mm256_set_epi32(0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF)
#define VECTOR_LOAD _mm256_load_pd
#define VECTOR_BIT_AND _mm256_and_pd
#define VECTOR_BIT_OR _mm256_or_pd
#define VECTOR_STORE _mm256_store_pd
#define VECTOR_AND_NOT _mm256_andnot_pd
#define BYTE_ALIGNMENT 32
#endif
#if !(defined(__SIM_SSE3) || defined(__AVX))
#define BYTE_ALIGNMENT 16
#endif
static void *malloc_aligned(size_t size, size_t align)
{
void *ptr = (void *)NULL;
int res;
#if defined (__APPLE__)
/*
presumably malloc on MACs always returns
a 16-byte aligned pointer
*/
ptr = malloc(size);
if(ptr == (void*)NULL)
assert(0);
#else
res = posix_memalign( &ptr, align, size );
if(res != 0)
assert(0);
#endif
return ptr;
}
/********************************DNA FUNCTIONS *****************************************************************/
static void hookupParsimony(nodeptr p, nodeptr q)
{
p->back = q;
q->back = p;
}
static void getxnodeLocal (nodeptr p)
{
nodeptr s;
if((s = p->next)->x || (s = s->next)->x)
{
p->x = s->x;
s->x = 0;
}
}
static void computeTraversalInfoParsimony(nodeptr p, int *ti, int *counter, int maxTips, boolean full)
{
nodeptr
q = p->next->back,
r = p->next->next->back;
if(! p->x)
getxnodeLocal(p);
if(full)
{
if(q->number > maxTips)
computeTraversalInfoParsimony(q, ti, counter, maxTips, full);
if(r->number > maxTips)
computeTraversalInfoParsimony(r, ti, counter, maxTips, full);
}
else
{
if(q->number > maxTips && !q->x)
computeTraversalInfoParsimony(q, ti, counter, maxTips, full);
if(r->number > maxTips && !r->x)
computeTraversalInfoParsimony(r, ti, counter, maxTips, full);
}
ti[*counter] = p->number;
ti[*counter + 1] = q->number;
ti[*counter + 2] = r->number;
*counter = *counter + 4;
}
#define BIT_COUNT(x) precomputed16_bitcount(x)
#if (defined(__SIM_SSE3) || defined(__AVX))
static inline unsigned int populationCount(INT_TYPE v_N)
{
unsigned int
res[INTS_PER_VECTOR] __attribute__ ((aligned (BYTE_ALIGNMENT)));
unsigned int
i,
a = 0;
VECTOR_STORE((CAST)res, v_N);
for(i = 0; i < INTS_PER_VECTOR; i++)
a += BIT_COUNT(res[i]);
return a;
}
#else
static inline unsigned int populationCount(unsigned int n)
{
return BIT_COUNT(n);
}
#endif
#if (defined(__SIM_SSE3) || defined(__AVX))
static void newviewParsimonyIterativeFast(tree *tr)
{
INT_TYPE
allOne = SET_ALL_BITS_ONE;
int
*ti = tr->ti,
count = ti[0],
index;
unsigned int
width = tr->compressedWidth;
for(index = 4; index < count; index += 4)
{
int
pNumber = ti[index],
qNumber = ti[index + 1],
rNumber = ti[index + 2];
parsimonyNumber
*leftState_A = tr->parsimonyState_A[qNumber],
*rightState_A = tr->parsimonyState_A[rNumber],
*thisState_A = tr->parsimonyState_A[pNumber],
*leftState_C = tr->parsimonyState_C[qNumber],
*rightState_C = tr->parsimonyState_C[rNumber],
*thisState_C = tr->parsimonyState_C[pNumber],
*leftState_G = tr->parsimonyState_G[qNumber],
*rightState_G = tr->parsimonyState_G[rNumber],
*thisState_G = tr->parsimonyState_G[pNumber],
*leftState_T = tr->parsimonyState_T[qNumber],
*rightState_T = tr->parsimonyState_T[rNumber],
*thisState_T = tr->parsimonyState_T[pNumber];
unsigned int
i,
ts = 0;
#pragma omp parallel for reduction(+:ts)
for(i = 0; i < width; i += INTS_PER_VECTOR)
{
INT_TYPE
s_r, s_l, v_N,
l_A, l_C, l_G, l_T,
v_A, v_C, v_G, v_T;
s_l = VECTOR_LOAD((CAST)(&leftState_A[i]));
s_r = VECTOR_LOAD((CAST)(&rightState_A[i]));
l_A = VECTOR_BIT_AND(s_l, s_r);
v_A = VECTOR_BIT_OR(s_l, s_r);
s_l = VECTOR_LOAD((CAST)(&leftState_C[i]));
s_r = VECTOR_LOAD((CAST)(&rightState_C[i]));
l_C = VECTOR_BIT_AND(s_l, s_r);
v_C = VECTOR_BIT_OR(s_l, s_r);
s_l = VECTOR_LOAD((CAST)(&leftState_G[i]));
s_r = VECTOR_LOAD((CAST)(&rightState_G[i]));
l_G = VECTOR_BIT_AND(s_l, s_r);
v_G = VECTOR_BIT_OR(s_l, s_r);
s_l = VECTOR_LOAD((CAST)(&leftState_T[i]));
s_r = VECTOR_LOAD((CAST)(&rightState_T[i]));
l_T = VECTOR_BIT_AND(s_l, s_r);
v_T = VECTOR_BIT_OR(s_l, s_r);
v_N = VECTOR_BIT_OR(VECTOR_BIT_OR(l_A, l_C), VECTOR_BIT_OR(l_G, l_T));
VECTOR_STORE((CAST)(&thisState_A[i]), VECTOR_BIT_OR(l_A, VECTOR_AND_NOT(v_N, v_A)));
VECTOR_STORE((CAST)(&thisState_C[i]), VECTOR_BIT_OR(l_C, VECTOR_AND_NOT(v_N, v_C)));
VECTOR_STORE((CAST)(&thisState_G[i]), VECTOR_BIT_OR(l_G, VECTOR_AND_NOT(v_N, v_G)));
VECTOR_STORE((CAST)(&thisState_T[i]), VECTOR_BIT_OR(l_T, VECTOR_AND_NOT(v_N, v_T)));
v_N = VECTOR_AND_NOT(v_N, allOne);
ts += populationCount(v_N);
}
tr->parsimonyScore[pNumber] = ts + tr->parsimonyScore[rNumber] + tr->parsimonyScore[qNumber];
}
}
static unsigned int evaluateParsimonyIterativeFast(tree *tr)
{
INT_TYPE
allOne = SET_ALL_BITS_ONE;
int
pNumber = tr->ti[1],
qNumber = tr->ti[2];
unsigned int
bestScore = tr->bestParsimony,
width = tr->compressedWidth,
i,
sum;
parsimonyNumber
*rightState_A = tr->parsimonyState_A[pNumber],
*leftState_A = tr->parsimonyState_A[qNumber],
*rightState_C = tr->parsimonyState_C[pNumber],
*leftState_C = tr->parsimonyState_C[qNumber],
*rightState_G = tr->parsimonyState_G[pNumber],
*leftState_G = tr->parsimonyState_G[qNumber],
*rightState_T = tr->parsimonyState_T[pNumber],
*leftState_T = tr->parsimonyState_T[qNumber];
if(tr->ti[0] > 4)
newviewParsimonyIterativeFast(tr);
sum = tr->parsimonyScore[pNumber] + tr->parsimonyScore[qNumber];
#pragma omp parallel for reduction(+:sum)
for(i = 0; i < width; i += INTS_PER_VECTOR)
{
INT_TYPE
l_A = VECTOR_BIT_AND(VECTOR_LOAD((CAST)(&leftState_A[i])), VECTOR_LOAD((CAST)(&rightState_A[i]))),
l_C = VECTOR_BIT_AND(VECTOR_LOAD((CAST)(&leftState_C[i])), VECTOR_LOAD((CAST)(&rightState_C[i]))),
l_G = VECTOR_BIT_AND(VECTOR_LOAD((CAST)(&leftState_G[i])), VECTOR_LOAD((CAST)(&rightState_G[i]))),
l_T = VECTOR_BIT_AND(VECTOR_LOAD((CAST)(&leftState_T[i])), VECTOR_LOAD((CAST)(&rightState_T[i]))),
v_N = VECTOR_BIT_OR(VECTOR_BIT_OR(l_A, l_C), VECTOR_BIT_OR(l_G, l_T));
v_N = VECTOR_AND_NOT(v_N, allOne);
sum += populationCount(v_N);
#ifndef _OPENMP
if(sum >= bestScore)
break;
#endif
}
return sum;
}
#else
static void newviewParsimonyIterativeFast(tree *tr)
{
int
count = tr->ti[0],
*ti = tr->ti,
index;
unsigned int
width = tr->compressedWidth;
for(index = 4; index < count; index += 4)
{
int
pNumber = ti[index],
qNumber = ti[index + 1],
rNumber = ti[index + 2];
parsimonyNumber
*leftState_A = tr->parsimonyState_A[qNumber],
*rightState_A = tr->parsimonyState_A[rNumber],
*thisState_A = tr->parsimonyState_A[pNumber],
*leftState_C = tr->parsimonyState_C[qNumber],
*rightState_C = tr->parsimonyState_C[rNumber],
*thisState_C = tr->parsimonyState_C[pNumber],
*leftState_G = tr->parsimonyState_G[qNumber],
*rightState_G = tr->parsimonyState_G[rNumber],
*thisState_G = tr->parsimonyState_G[pNumber],
*leftState_T = tr->parsimonyState_T[qNumber],
*rightState_T = tr->parsimonyState_T[rNumber],
*thisState_T = tr->parsimonyState_T[pNumber];
register parsimonyNumber
o_A,
o_C,
o_G,
o_T,
t_A,
t_C,
t_G,
t_T,
t_N;
unsigned int
i,
ts = 0;
for(i = 0; i < width; i++)
{
t_A = leftState_A[i] & rightState_A[i];
t_C = leftState_C[i] & rightState_C[i];
t_G = leftState_G[i] & rightState_G[i];
t_T = leftState_T[i] & rightState_T[i];
o_A = leftState_A[i] | rightState_A[i];
o_C = leftState_C[i] | rightState_C[i];
o_G = leftState_G[i] | rightState_G[i];
o_T = leftState_T[i] | rightState_T[i];
t_N = ~(t_A | t_C | t_G | t_T);
thisState_A[i] = t_A | (t_N & o_A);
thisState_C[i] = t_C | (t_N & o_C);
thisState_G[i] = t_G | (t_N & o_G);
thisState_T[i] = t_T | (t_N & o_T);
ts += populationCount(t_N);
}
tr->parsimonyScore[pNumber] = ts + tr->parsimonyScore[rNumber] + tr->parsimonyScore[qNumber];
}
}
static unsigned int evaluateParsimonyIterativeFast(tree *tr)
{
int
pNumber = tr->ti[1],
qNumber = tr->ti[2];
unsigned int
bestScore = tr->bestParsimony,
width = tr->compressedWidth,
i,
sum,
t_A,
t_C,
t_G,
t_T,
t_N;
parsimonyNumber
*rightState_A = tr->parsimonyState_A[pNumber],
*leftState_A = tr->parsimonyState_A[qNumber],
*rightState_C = tr->parsimonyState_C[pNumber],
*leftState_C = tr->parsimonyState_C[qNumber],
*rightState_G = tr->parsimonyState_G[pNumber],
*leftState_G = tr->parsimonyState_G[qNumber],
*rightState_T = tr->parsimonyState_T[pNumber],
*leftState_T = tr->parsimonyState_T[qNumber];
if(tr->ti[0] > 4)
newviewParsimonyIterativeFast(tr);
sum = tr->parsimonyScore[pNumber] + tr->parsimonyScore[qNumber];
for(i = 0; i < width; i++)
{
t_A = leftState_A[i] & rightState_A[i];
t_C = leftState_C[i] & rightState_C[i];
t_G = leftState_G[i] & rightState_G[i];
t_T = leftState_T[i] & rightState_T[i];
t_N = ~(t_A | t_C | t_G | t_T);
sum += populationCount(t_N);
if(sum >= bestScore)
break;
}
return sum;
}
#endif
static unsigned int evaluateParsimony(tree *tr, nodeptr p, boolean full)
{
volatile unsigned int result;
nodeptr q = p->back;
int
*ti = tr->ti,
counter = 4;
ti[1] = p->number;
ti[2] = q->number;
if(full)
{
if(p->number > tr->mxtips)
computeTraversalInfoParsimony(p, ti, &counter, tr->mxtips, full);
if(q->number > tr->mxtips)
computeTraversalInfoParsimony(q, ti, &counter, tr->mxtips, full);
}
else
{
if(p->number > tr->mxtips && !p->x)
computeTraversalInfoParsimony(p, ti, &counter, tr->mxtips, full);
if(q->number > tr->mxtips && !q->x)
computeTraversalInfoParsimony(q, ti, &counter, tr->mxtips, full);
}
ti[0] = counter;
result = evaluateParsimonyIterativeFast(tr);
return result;
}
static void newviewParsimony(tree *tr, nodeptr p)
{
if(p->number <= tr->mxtips)
return;
{
int
counter = 4;
computeTraversalInfoParsimony(p, tr->ti, &counter, tr->mxtips, FALSE);
tr->ti[0] = counter;
newviewParsimonyIterativeFast(tr);
}
}
/****************************************************************************************************************************************/
static void insertParsimony (tree *tr, nodeptr p, nodeptr q)
{
nodeptr r;
r = q->back;
hookupParsimony(p->next, q);
hookupParsimony(p->next->next, r);
newviewParsimony(tr, p);
}
static nodeptr buildNewTip (tree *tr, nodeptr p)
{
nodeptr q;
q = tr->nodep[(tr->nextnode)++];
hookupParsimony(p, q);
q->next->back = (nodeptr)NULL;
q->next->next->back = (nodeptr)NULL;
return q;
}
static void buildSimpleTree (tree *tr, int ip, int iq, int ir)
{
nodeptr p, s;
int i;
i = MIN(ip, iq);
if (ir < i) i = ir;
tr->start = tr->nodep[i];
tr->ntips = 3;
p = tr->nodep[ip];
hookupParsimony(p, tr->nodep[iq]);
s = buildNewTip(tr, tr->nodep[ir]);
insertParsimony(tr, s, p);
}
static void testInsertParsimony (tree *tr, nodeptr p, nodeptr q)
{
unsigned int mp;
nodeptr r = q->back;
insertParsimony(tr, p, q);
mp = evaluateParsimony(tr, p->next->next, FALSE);
if(mp < tr->bestParsimony)
{
tr->bestParsimony = mp;
tr->insertNode = q;
tr->removeNode = p;
}
hookupParsimony(q, r);
p->next->next->back = p->next->back = (nodeptr) NULL;
return;
}
static void restoreTreeParsimony(tree *tr, nodeptr p, nodeptr q)
{
nodeptr
r = q->back;
int counter = 4;
hookupParsimony(p->next, q);
hookupParsimony(p->next->next, r);
computeTraversalInfoParsimony(p, tr->ti, &counter, tr->mxtips, FALSE);
tr->ti[0] = counter;
newviewParsimonyIterativeFast(tr);
}
static void addTraverseParsimony (tree *tr, nodeptr p, nodeptr q, int mintrav, int maxtrav, boolean doAll)
{
if (doAll || (--mintrav <= 0))
testInsertParsimony(tr, p, q);
if (((q->number > tr->mxtips)) && ((--maxtrav > 0) || doAll))
{
addTraverseParsimony(tr, p, q->next->back, mintrav, maxtrav, doAll);
addTraverseParsimony(tr, p, q->next->next->back, mintrav, maxtrav, doAll);
}
}
static nodeptr findAnyTipFast(nodeptr p, int numsp)
{
return (p->number <= numsp)? p : findAnyTipFast(p->next->back, numsp);
}
static double randum(long *seed)
{
long sum, mult0, mult1, seed0, seed1, seed2, newseed0, newseed1, newseed2;
double res;
mult0 = 1549;
seed0 = *seed & 4095;
sum = mult0 * seed0;
newseed0 = sum & 4095;
sum >>= 12;
seed1 = (*seed >> 12) & 4095;
mult1 = 406;
sum += mult0 * seed1 + mult1 * seed0;
newseed1 = sum & 4095;
sum >>= 12;
seed2 = (*seed >> 24) & 255;
sum += mult0 * seed2 + mult1 * seed1;
newseed2 = sum & 255;
*seed = newseed2 << 24 | newseed1 << 12 | newseed0;
res = 0.00390625 * (newseed2 + 0.000244140625 * (newseed1 + 0.000244140625 * newseed0));
return res;
}
static void makePermutationFast(int *perm, int n, analdef *adef)
{
int i, j, k;
assert(adef->parsimonySeed != 0);
for (i = 1; i <= n; i++)
perm[i] = i;
for (i = 1; i <= n; i++)
{
double d = randum(&adef->parsimonySeed);
k = (int)((double)(n + 1 - i) * d);
j = perm[i];
perm[i] = perm[i + k];
perm[i + k] = j;
}
}
static nodeptr removeNodeParsimony (nodeptr p)
{
nodeptr q, r;
q = p->next->back;
r = p->next->next->back;
hookupParsimony(q, r);
p->next->next->back = p->next->back = (node *) NULL;
return q;
}
static int rearrangeParsimony(tree *tr, nodeptr p, int mintrav, int maxtrav, boolean doAll)
{
nodeptr p1, p2, q, q1, q2;
int mintrav2;
if (maxtrav > tr->ntips - 3)
maxtrav = tr->ntips - 3;
if(maxtrav < mintrav)
return 0;
q = p->back;
if(p->number > tr->mxtips)
{
p1 = p->next->back;
p2 = p->next->next->back;
if ((p1->number > tr->mxtips) || (p2->number > tr->mxtips))
{
removeNodeParsimony(p);
if ((p1->number > tr->mxtips))
{
addTraverseParsimony(tr, p, p1->next->back, mintrav, maxtrav, doAll);
addTraverseParsimony(tr, p, p1->next->next->back, mintrav, maxtrav, doAll);
}
if ((p2->number > tr->mxtips))
{
addTraverseParsimony(tr, p, p2->next->back, mintrav, maxtrav, doAll);
addTraverseParsimony(tr, p, p2->next->next->back, mintrav, maxtrav, doAll);
}
hookupParsimony(p->next, p1);
hookupParsimony(p->next->next, p2);
newviewParsimony(tr, p);
}
}
if ((q->number > tr->mxtips) && maxtrav > 0)
{
q1 = q->next->back;
q2 = q->next->next->back;
if (
(
(q1->number > tr->mxtips) &&
((q1->next->back->number > tr->mxtips) || (q1->next->next->back->number > tr->mxtips))
)
||
(
(q2->number > tr->mxtips) &&
((q2->next->back->number > tr->mxtips) || (q2->next->next->back->number > tr->mxtips))
)
)
{
removeNodeParsimony(q);
mintrav2 = mintrav > 2 ? mintrav : 2;
if ((q1->number > tr->mxtips))
{
addTraverseParsimony(tr, q, q1->next->back, mintrav2 , maxtrav, doAll);
addTraverseParsimony(tr, q, q1->next->next->back, mintrav2 , maxtrav, doAll);
}
if ((q2->number > tr->mxtips))
{
addTraverseParsimony(tr, q, q2->next->back, mintrav2 , maxtrav, doAll);
addTraverseParsimony(tr, q, q2->next->next->back, mintrav2 , maxtrav, doAll);
}
hookupParsimony(q->next, q1);
hookupParsimony(q->next->next, q2);
newviewParsimony(tr, q);
}
}
return 1;
}
static void restoreTreeRearrangeParsimony(tree *tr)
{
removeNodeParsimony(tr->removeNode);
restoreTreeParsimony(tr, tr->removeNode, tr->insertNode);
}
static boolean isInformative(tree *tr, int site)
{
int
informativeCounter = 0,
check[256],
j,
undetermined = 15;
unsigned char
nucleotide,
target = 0;
for(j = 0; j < 256; j++)
check[j] = 0;
for(j = 1; j <= tr->mxtips; j++)
{
nucleotide = tr->yVector[j][site];
check[nucleotide] = check[nucleotide] + 1;
}
if(check[1] > 1)
{
informativeCounter++;
target = target | 1;
}
if(check[2] > 1)
{
informativeCounter++;
target = target | 2;
}
if(check[4] > 1)
{
informativeCounter++;
target = target | 4;
}
if(check[8] > 1)
{
informativeCounter++;
target = target | 8;
}
if(informativeCounter >= 2)
return TRUE;
else
{
for(j = 0; j < undetermined; j++)
{
if(j == 3 || j == 5 || j == 6 || j == 7 || j == 9 || j == 10 || j == 11 ||
j == 12 || j == 13 || j == 14)
{
if(check[j] > 1)
{
if(!(target & j))
return TRUE;
}
}
}
}
return FALSE;
}
static void determineUninformativeSites(tree *tr, int *informative)
{
int
i,
number = 0;
/*
Not all characters are useful in constructing a parsimony tree.
Invariant characters, those that have the same state in all taxa,
are obviously useless and are ignored by the method. Characters in
which a state occurs in only one taxon are also ignored.
All these characters are called parsimony uninformative.
Alternative definition: informative columns contain at least two types
of nucleotides, and each nucleotide must appear at least twice in each
column. Kind of a pain if we intend to check for this when using, e.g.,
amibiguous DNA encoding.
*/
for(i = 0; i < tr->cdta->endsite; i++)
{
if(isInformative(tr, i))
informative[i] = 1;
else
{
informative[i] = 0;
number++;
}
}
/* printf("Uninformative Patterns: %d\n", number); */
}
static void reorderNodes(tree *tr, nodeptr *np, nodeptr p, int *count)
{
int i, found = 0;
if((p->number <= tr->mxtips))
return;
else
{
for(i = tr->mxtips + 1; (i <= (tr->mxtips + tr->mxtips - 1)) && (found == 0); i++)
{
if (p == np[i] || p == np[i]->next || p == np[i]->next->next)
{
if(p == np[i])
tr->nodep[*count + tr->mxtips + 1] = np[i];
else
{
if(p == np[i]->next)
tr->nodep[*count + tr->mxtips + 1] = np[i]->next;
else
tr->nodep[*count + tr->mxtips + 1] = np[i]->next->next;
}
found = 1;
*count = *count + 1;
}
}
reorderNodes(tr, np, p->next->back, count);
reorderNodes(tr, np, p->next->next->back, count);
}
}
static void nodeRectifierFast(tree *tr)
{
nodeptr *np = (nodeptr *)malloc(2 * (size_t)tr->mxtips * sizeof(nodeptr));
int i;
int count = 0;
tr->start = tr->nodep[1];
for(i = tr->mxtips + 1; i <= (tr->mxtips + tr->mxtips - 1); i++)
np[i] = tr->nodep[i];
reorderNodes(tr, np, tr->start->back, &count);
free(np);
}
static parsimonyNumber *compressDNA(tree *tr, int *informative)
{
size_t
i,
entries = 0,
compressedEntries,
compressedEntriesPadded;
parsimonyNumber
*compressedScratch;