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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 __AVX
#ifdef __SIM_SSE3
#define _SSE3_WAS_DEFINED
#undef __SIM_SSE3
#endif
#endif
#ifdef __SIM_SSE3
#include <xmmintrin.h>
#include <pmmintrin.h>
#endif
#ifdef __AVX
#include <xmmintrin.h>
#include <immintrin.h>
#endif
#include "axml.h"
extern const unsigned int mask32[32];
/* vector-specific stuff */
extern char **globalArgv;
extern int globalArgc;
#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 SET_ALL_BITS_ZERO _mm_set_epi32(0x00000000, 0x00000000, 0x00000000, 0x00000000)
#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
#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 SET_ALL_BITS_ZERO (__m256d)_mm256_set_epi32(0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000000)
#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
#endif
extern double masterTime;
extern char workdir[1024];
extern char run_id[128];
/********************************DNA FUNCTIONS *****************************************************************/
static void checkSeed(analdef *adef)
{
static boolean seedChecked = FALSE;
if(!seedChecked)
{
/*printf("Checking seed\n");*/
if(adef->parsimonySeed <= 0)
{
printf("Error: you need to specify a random number seed with \"-p\" for the randomized stepwise addition\n");
printf("parsimony algorithm or random tree building algorithm such that runs can be reproduced and debugged ... exiting\n");
}
assert(adef->parsimonySeed > 0);
seedChecked = TRUE;
}
}
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;
}
#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))
void newviewParsimonyIterativeFast(tree *tr)
{
INT_TYPE
allOne = SET_ALL_BITS_ONE;
int
model,
*ti = tr->ti,
count = ti[0],
index;
for(index = 4; index < count; index += 4)
{
unsigned int
totalScore = 0;
size_t
pNumber = (size_t)ti[index],
qNumber = (size_t)ti[index + 1],
rNumber = (size_t)ti[index + 2];
for(model = 0; model < tr->NumberOfModels; model++)
{
size_t
k,
states = tr->partitionData[model].states,
width = tr->partitionData[model].parsimonyLength;
unsigned int
i;
switch(states)
{
case 2:
{
parsimonyNumber
*left[2],
*right[2],
*thisOne[2];
for(k = 0; k < 2; k++)
{
left[k] = &(tr->partitionData[model].parsVect[(width * 2 * qNumber) + width * k]);
right[k] = &(tr->partitionData[model].parsVect[(width * 2 * rNumber) + width * k]);
thisOne[k] = &(tr->partitionData[model].parsVect[(width * 2 * pNumber) + width * k]);
}
for(i = 0; i < width; i += INTS_PER_VECTOR)
{
INT_TYPE
s_r, s_l, v_N,
l_A, l_C,
v_A, v_C;
s_l = VECTOR_LOAD((CAST)(&left[0][i]));
s_r = VECTOR_LOAD((CAST)(&right[0][i]));
l_A = VECTOR_BIT_AND(s_l, s_r);
v_A = VECTOR_BIT_OR(s_l, s_r);
s_l = VECTOR_LOAD((CAST)(&left[1][i]));
s_r = VECTOR_LOAD((CAST)(&right[1][i]));
l_C = VECTOR_BIT_AND(s_l, s_r);
v_C = VECTOR_BIT_OR(s_l, s_r);
v_N = VECTOR_BIT_OR(l_A, l_C);
VECTOR_STORE((CAST)(&thisOne[0][i]), VECTOR_BIT_OR(l_A, VECTOR_AND_NOT(v_N, v_A)));
VECTOR_STORE((CAST)(&thisOne[1][i]), VECTOR_BIT_OR(l_C, VECTOR_AND_NOT(v_N, v_C)));
v_N = VECTOR_AND_NOT(v_N, allOne);
totalScore += populationCount(v_N);
}
}
break;
case 4:
{
parsimonyNumber
*left[4],
*right[4],
*thisOne[4];
for(k = 0; k < 4; k++)
{
left[k] = &(tr->partitionData[model].parsVect[(width * 4 * qNumber) + width * k]);
right[k] = &(tr->partitionData[model].parsVect[(width * 4 * rNumber) + width * k]);
thisOne[k] = &(tr->partitionData[model].parsVect[(width * 4 * pNumber) + width * k]);
}
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)(&left[0][i]));
s_r = VECTOR_LOAD((CAST)(&right[0][i]));
l_A = VECTOR_BIT_AND(s_l, s_r);
v_A = VECTOR_BIT_OR(s_l, s_r);
s_l = VECTOR_LOAD((CAST)(&left[1][i]));
s_r = VECTOR_LOAD((CAST)(&right[1][i]));
l_C = VECTOR_BIT_AND(s_l, s_r);
v_C = VECTOR_BIT_OR(s_l, s_r);
s_l = VECTOR_LOAD((CAST)(&left[2][i]));
s_r = VECTOR_LOAD((CAST)(&right[2][i]));
l_G = VECTOR_BIT_AND(s_l, s_r);
v_G = VECTOR_BIT_OR(s_l, s_r);
s_l = VECTOR_LOAD((CAST)(&left[3][i]));
s_r = VECTOR_LOAD((CAST)(&right[3][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)(&thisOne[0][i]), VECTOR_BIT_OR(l_A, VECTOR_AND_NOT(v_N, v_A)));
VECTOR_STORE((CAST)(&thisOne[1][i]), VECTOR_BIT_OR(l_C, VECTOR_AND_NOT(v_N, v_C)));
VECTOR_STORE((CAST)(&thisOne[2][i]), VECTOR_BIT_OR(l_G, VECTOR_AND_NOT(v_N, v_G)));
VECTOR_STORE((CAST)(&thisOne[3][i]), VECTOR_BIT_OR(l_T, VECTOR_AND_NOT(v_N, v_T)));
v_N = VECTOR_AND_NOT(v_N, allOne);
totalScore += populationCount(v_N);
}
}
break;
case 20:
{
parsimonyNumber
*left[20],
*right[20],
*thisOne[20];
for(k = 0; k < 20; k++)
{
left[k] = &(tr->partitionData[model].parsVect[(width * 20 * qNumber) + width * k]);
right[k] = &(tr->partitionData[model].parsVect[(width * 20 * rNumber) + width * k]);
thisOne[k] = &(tr->partitionData[model].parsVect[(width * 20 * pNumber) + width * k]);
}
for(i = 0; i < width; i += INTS_PER_VECTOR)
{
size_t j;
INT_TYPE
s_r, s_l,
v_N = SET_ALL_BITS_ZERO,
l_A[20],
v_A[20];
for(j = 0; j < 20; j++)
{
s_l = VECTOR_LOAD((CAST)(&left[j][i]));
s_r = VECTOR_LOAD((CAST)(&right[j][i]));
l_A[j] = VECTOR_BIT_AND(s_l, s_r);
v_A[j] = VECTOR_BIT_OR(s_l, s_r);
v_N = VECTOR_BIT_OR(v_N, l_A[j]);
}
for(j = 0; j < 20; j++)
VECTOR_STORE((CAST)(&thisOne[j][i]), VECTOR_BIT_OR(l_A[j], VECTOR_AND_NOT(v_N, v_A[j])));
v_N = VECTOR_AND_NOT(v_N, allOne);
totalScore += populationCount(v_N);
}
}
break;
default:
{
parsimonyNumber
*left[32],
*right[32],
*thisOne[32];
assert(states <= 32);
for(k = 0; k < states; k++)
{
left[k] = &(tr->partitionData[model].parsVect[(width * states * qNumber) + width * k]);
right[k] = &(tr->partitionData[model].parsVect[(width * states * rNumber) + width * k]);
thisOne[k] = &(tr->partitionData[model].parsVect[(width * states * pNumber) + width * k]);
}
for(i = 0; i < width; i += INTS_PER_VECTOR)
{
size_t j;
INT_TYPE
s_r, s_l,
v_N = SET_ALL_BITS_ZERO,
l_A[32],
v_A[32];
for(j = 0; j < states; j++)
{
s_l = VECTOR_LOAD((CAST)(&left[j][i]));
s_r = VECTOR_LOAD((CAST)(&right[j][i]));
l_A[j] = VECTOR_BIT_AND(s_l, s_r);
v_A[j] = VECTOR_BIT_OR(s_l, s_r);
v_N = VECTOR_BIT_OR(v_N, l_A[j]);
}
for(j = 0; j < states; j++)
VECTOR_STORE((CAST)(&thisOne[j][i]), VECTOR_BIT_OR(l_A[j], VECTOR_AND_NOT(v_N, v_A[j])));
v_N = VECTOR_AND_NOT(v_N, allOne);
totalScore += populationCount(v_N);
}
}
}
}
tr->parsimonyScore[pNumber] = totalScore + tr->parsimonyScore[rNumber] + tr->parsimonyScore[qNumber];
}
}
unsigned int evaluateParsimonyIterativeFast(tree *tr)
{
INT_TYPE
allOne = SET_ALL_BITS_ONE;
size_t
pNumber = (size_t)tr->ti[1],
qNumber = (size_t)tr->ti[2];
int
model;
unsigned int
bestScore = tr->bestParsimony,
sum;
if(tr->ti[0] > 4)
newviewParsimonyIterativeFast(tr);
sum = tr->parsimonyScore[pNumber] + tr->parsimonyScore[qNumber];
for(model = 0; model < tr->NumberOfModels; model++)
{
size_t
k,
states = tr->partitionData[model].states,
width = tr->partitionData[model].parsimonyLength,
i;
switch(states)
{
case 2:
{
parsimonyNumber
*left[2],
*right[2];
for(k = 0; k < 2; k++)
{
left[k] = &(tr->partitionData[model].parsVect[(width * 2 * qNumber) + width * k]);
right[k] = &(tr->partitionData[model].parsVect[(width * 2 * pNumber) + width * k]);
}
for(i = 0; i < width; i += INTS_PER_VECTOR)
{
INT_TYPE
l_A = VECTOR_BIT_AND(VECTOR_LOAD((CAST)(&left[0][i])), VECTOR_LOAD((CAST)(&right[0][i]))),
l_C = VECTOR_BIT_AND(VECTOR_LOAD((CAST)(&left[1][i])), VECTOR_LOAD((CAST)(&right[1][i]))),
v_N = VECTOR_BIT_OR(l_A, l_C);
v_N = VECTOR_AND_NOT(v_N, allOne);
sum += populationCount(v_N);
if(sum >= bestScore)
return sum;
}
}
break;
case 4:
{
parsimonyNumber
*left[4],
*right[4];
for(k = 0; k < 4; k++)
{
left[k] = &(tr->partitionData[model].parsVect[(width * 4 * qNumber) + width * k]);
right[k] = &(tr->partitionData[model].parsVect[(width * 4 * pNumber) + width * k]);
}
for(i = 0; i < width; i += INTS_PER_VECTOR)
{
INT_TYPE
l_A = VECTOR_BIT_AND(VECTOR_LOAD((CAST)(&left[0][i])), VECTOR_LOAD((CAST)(&right[0][i]))),
l_C = VECTOR_BIT_AND(VECTOR_LOAD((CAST)(&left[1][i])), VECTOR_LOAD((CAST)(&right[1][i]))),
l_G = VECTOR_BIT_AND(VECTOR_LOAD((CAST)(&left[2][i])), VECTOR_LOAD((CAST)(&right[2][i]))),
l_T = VECTOR_BIT_AND(VECTOR_LOAD((CAST)(&left[3][i])), VECTOR_LOAD((CAST)(&right[3][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);
if(sum >= bestScore)
return sum;
}
}
break;
case 20:
{
parsimonyNumber
*left[20],
*right[20];
for(k = 0; k < 20; k++)
{
left[k] = &(tr->partitionData[model].parsVect[(width * 20 * qNumber) + width * k]);
right[k] = &(tr->partitionData[model].parsVect[(width * 20 * pNumber) + width * k]);
}
for(i = 0; i < width; i += INTS_PER_VECTOR)
{
int
j;
INT_TYPE
l_A,
v_N = SET_ALL_BITS_ZERO;
for(j = 0; j < 20; j++)
{
l_A = VECTOR_BIT_AND(VECTOR_LOAD((CAST)(&left[j][i])), VECTOR_LOAD((CAST)(&right[j][i])));
v_N = VECTOR_BIT_OR(l_A, v_N);
}
v_N = VECTOR_AND_NOT(v_N, allOne);
sum += populationCount(v_N);
if(sum >= bestScore)
return sum;
}
}
break;
default:
{
parsimonyNumber
*left[32],
*right[32];
assert(states <= 32);
for(k = 0; k < states; k++)
{
left[k] = &(tr->partitionData[model].parsVect[(width * states * qNumber) + width * k]);
right[k] = &(tr->partitionData[model].parsVect[(width * states * pNumber) + width * k]);
}
for(i = 0; i < width; i += INTS_PER_VECTOR)
{
size_t
j;
INT_TYPE
l_A,
v_N = SET_ALL_BITS_ZERO;
for(j = 0; j < states; j++)
{
l_A = VECTOR_BIT_AND(VECTOR_LOAD((CAST)(&left[j][i])), VECTOR_LOAD((CAST)(&right[j][i])));
v_N = VECTOR_BIT_OR(l_A, v_N);
}
v_N = VECTOR_AND_NOT(v_N, allOne);
sum += populationCount(v_N);
if(sum >= bestScore)
return sum;
}
}
}
}
return sum;
}
#else
void newviewParsimonyIterativeFast(tree *tr)
{
int
model,
*ti = tr->ti,
count = ti[0],
index;
for(index = 4; index < count; index += 4)
{
unsigned int
totalScore = 0;
size_t
pNumber = (size_t)ti[index],
qNumber = (size_t)ti[index + 1],
rNumber = (size_t)ti[index + 2];
for(model = 0; model < tr->NumberOfModels; model++)
{
size_t
k,
states = tr->partitionData[model].states,
width = tr->partitionData[model].parsimonyLength;
unsigned int
i;
switch(states)
{
case 2:
{
parsimonyNumber
*left[2],
*right[2],
*thisOne[2];
parsimonyNumber
o_A,
o_C,
t_A,
t_C,
t_N;
for(k = 0; k < 2; k++)
{
left[k] = &(tr->partitionData[model].parsVect[(width * 2 * qNumber) + width * k]);
right[k] = &(tr->partitionData[model].parsVect[(width * 2 * rNumber) + width * k]);
thisOne[k] = &(tr->partitionData[model].parsVect[(width * 2 * pNumber) + width * k]);
}
for(i = 0; i < width; i++)
{
t_A = left[0][i] & right[0][i];
t_C = left[1][i] & right[1][i];
o_A = left[0][i] | right[0][i];
o_C = left[1][i] | right[1][i];
t_N = ~(t_A | t_C);
thisOne[0][i] = t_A | (t_N & o_A);
thisOne[1][i] = t_C | (t_N & o_C);
totalScore += populationCount(t_N);
}
}
break;
case 4:
{
parsimonyNumber
*left[4],
*right[4],
*thisOne[4];
for(k = 0; k < 4; k++)
{
left[k] = &(tr->partitionData[model].parsVect[(width * 4 * qNumber) + width * k]);
right[k] = &(tr->partitionData[model].parsVect[(width * 4 * rNumber) + width * k]);
thisOne[k] = &(tr->partitionData[model].parsVect[(width * 4 * pNumber) + width * k]);
}
parsimonyNumber
o_A,
o_C,
o_G,
o_T,
t_A,
t_C,
t_G,
t_T,
t_N;
for(i = 0; i < width; i++)
{
t_A = left[0][i] & right[0][i];
t_C = left[1][i] & right[1][i];
t_G = left[2][i] & right[2][i];
t_T = left[3][i] & right[3][i];
o_A = left[0][i] | right[0][i];
o_C = left[1][i] | right[1][i];
o_G = left[2][i] | right[2][i];
o_T = left[3][i] | right[3][i];
t_N = ~(t_A | t_C | t_G | t_T);
thisOne[0][i] = t_A | (t_N & o_A);
thisOne[1][i] = t_C | (t_N & o_C);
thisOne[2][i] = t_G | (t_N & o_G);
thisOne[3][i] = t_T | (t_N & o_T);
totalScore += populationCount(t_N);
}
}
break;
case 20:
{
parsimonyNumber
*left[20],
*right[20],
*thisOne[20];
parsimonyNumber
o_A[20],
t_A[20],
t_N;
for(k = 0; k < 20; k++)
{
left[k] = &(tr->partitionData[model].parsVect[(width * 20 * qNumber) + width * k]);
right[k] = &(tr->partitionData[model].parsVect[(width * 20 * rNumber) + width * k]);
thisOne[k] = &(tr->partitionData[model].parsVect[(width * 20 * pNumber) + width * k]);
}
for(i = 0; i < width; i++)
{
size_t k;
t_N = 0;
for(k = 0; k < 20; k++)
{
t_A[k] = left[k][i] & right[k][i];
o_A[k] = left[k][i] | right[k][i];
t_N = t_N | t_A[k];
}
t_N = ~t_N;
for(k = 0; k < 20; k++)
thisOne[k][i] = t_A[k] | (t_N & o_A[k]);
totalScore += populationCount(t_N);
}
}
break;
default:
{
parsimonyNumber
*left[32],
*right[32],
*thisOne[32];
parsimonyNumber
o_A[32],
t_A[32],
t_N;
assert(states <= 32);
for(k = 0; k < states; k++)
{
left[k] = &(tr->partitionData[model].parsVect[(width * states * qNumber) + width * k]);
right[k] = &(tr->partitionData[model].parsVect[(width * states * rNumber) + width * k]);
thisOne[k] = &(tr->partitionData[model].parsVect[(width * states * pNumber) + width * k]);
}
for(i = 0; i < width; i++)
{
t_N = 0;
for(k = 0; k < states; k++)
{
t_A[k] = left[k][i] & right[k][i];
o_A[k] = left[k][i] | right[k][i];
t_N = t_N | t_A[k];
}
t_N = ~t_N;
for(k = 0; k < states; k++)
thisOne[k][i] = t_A[k] | (t_N & o_A[k]);
totalScore += populationCount(t_N);
}
}
}
}
tr->parsimonyScore[pNumber] = totalScore + tr->parsimonyScore[rNumber] + tr->parsimonyScore[qNumber];
}
}
unsigned int evaluateParsimonyIterativeFast(tree *tr)
{
size_t
pNumber = (size_t)tr->ti[1],
qNumber = (size_t)tr->ti[2];
int
model;
unsigned int
bestScore = tr->bestParsimony,
sum;
if(tr->ti[0] > 4)
newviewParsimonyIterativeFast(tr);
sum = tr->parsimonyScore[pNumber] + tr->parsimonyScore[qNumber];
for(model = 0; model < tr->NumberOfModels; model++)
{
size_t
k,
states = tr->partitionData[model].states,
width = tr->partitionData[model].parsimonyLength,
i;
switch(states)
{
case 2:
{
parsimonyNumber
t_A,
t_C,
t_N,
*left[2],
*right[2];
for(k = 0; k < 2; k++)
{
left[k] = &(tr->partitionData[model].parsVect[(width * 2 * qNumber) + width * k]);
right[k] = &(tr->partitionData[model].parsVect[(width * 2 * pNumber) + width * k]);
}
for(i = 0; i < width; i++)
{
t_A = left[0][i] & right[0][i];
t_C = left[1][i] & right[1][i];
t_N = ~(t_A | t_C);
sum += populationCount(t_N);
if(sum >= bestScore)
return sum;
}
}
break;
case 4:
{
parsimonyNumber
t_A,
t_C,
t_G,
t_T,
t_N,
*left[4],
*right[4];
for(k = 0; k < 4; k++)
{
left[k] = &(tr->partitionData[model].parsVect[(width * 4 * qNumber) + width * k]);
right[k] = &(tr->partitionData[model].parsVect[(width * 4 * pNumber) + width * k]);
}
for(i = 0; i < width; i++)
{
t_A = left[0][i] & right[0][i];
t_C = left[1][i] & right[1][i];
t_G = left[2][i] & right[2][i];
t_T = left[3][i] & right[3][i];
t_N = ~(t_A | t_C | t_G | t_T);
sum += populationCount(t_N);
if(sum >= bestScore)
return sum;
}
}
break;
case 20:
{
parsimonyNumber
t_A,
t_N,
*left[20],
*right[20];
for(k = 0; k < 20; k++)
{
left[k] = &(tr->partitionData[model].parsVect[(width * 20 * qNumber) + width * k]);
right[k] = &(tr->partitionData[model].parsVect[(width * 20 * pNumber) + width * k]);
}
for(i = 0; i < width; i++)
{
t_N = 0;
for(k = 0; k < 20; k++)
{
t_A = left[k][i] & right[k][i];
t_N = t_N | t_A;
}
t_N = ~t_N;
sum += populationCount(t_N);
if(sum >= bestScore)
return sum;
}
}
break;
default:
{
parsimonyNumber
t_A,
t_N,
*left[32],
*right[32];
assert(states <= 32);
for(k = 0; k < states; k++)
{
left[k] = &(tr->partitionData[model].parsVect[(width * states * qNumber) + width * k]);
right[k] = &(tr->partitionData[model].parsVect[(width * states * pNumber) + width * k]);
}
for(i = 0; i < width; i++)
{
t_N = 0;
for(k = 0; k < states; k++)
{
t_A = left[k][i] & right[k][i];
t_N = t_N | t_A;
}
t_N = ~t_N;
sum += populationCount(t_N);
if(sum >= bestScore)
return sum;
}
}
}
}
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;
hookupDefault(p->next, q, tr->numBranches);
hookupDefault(p->next->next, r, tr->numBranches);
newviewParsimony(tr, p);
}
/*
static nodeptr buildNewTip (tree *tr, nodeptr p)
{
nodeptr q;
q = tr->nodep[(tr->nextnode)++];
hookupDefault(p, q, tr->numBranches);
q->next->back = (nodeptr)NULL;
q->next->next->back = (nodeptr)NULL;
assert(q == q->next->next->next);
assert(q->x || q->next->x || q->next->next->x);
return q;
}
*/
static nodeptr buildNewTip (tree *tr, nodeptr p)
{
nodeptr q;
q = tr->nodep[(tr->nextnode)++];
hookupDefault(p, q, tr->numBranches);
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];
hookupDefault(p, tr->nodep[iq], tr->numBranches);
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;
boolean
doIt = TRUE;
if(tr->grouped)
{
int
rNumber = tr->constraintVector[r->number],
qNumber = tr->constraintVector[q->number],
pNumber = tr->constraintVector[p->number];
doIt = FALSE;
if(pNumber == -9)
pNumber = checker(tr, p->back);
if(pNumber == -9)
doIt = TRUE;
else
{
if(qNumber == -9)
qNumber = checker(tr, q);
if(rNumber == -9)
rNumber = checker(tr, r);
if(pNumber == rNumber || pNumber == qNumber)
doIt = TRUE;
}
}
if(doIt)
{
insertParsimony(tr, p, q);
mp = evaluateParsimony(tr, p->next->next, FALSE);
if(mp < tr->bestParsimony)
{
tr->bestParsimony = mp;
tr->insertNode = q;
tr->removeNode = p;
}
hookupDefault(q, r, tr->numBranches);
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;
hookupDefault(p->next, q, tr->numBranches);
hookupDefault(p->next->next, r, tr->numBranches);
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 nodeptr removeNodeParsimony (nodeptr p, tree *tr)
{
nodeptr q, r;
q = p->next->back;
r = p->next->next->back;
hookupDefault(q, r, tr->numBranches);
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;
boolean
doP = TRUE,
doQ = TRUE;
if (maxtrav > tr->ntips - 3)
maxtrav = tr->ntips - 3;
assert(mintrav == 1);
if(maxtrav < mintrav)
return 0;
q = p->back;
if(tr->constrained)
{
if(! tipHomogeneityChecker(tr, p->back, 0))
doP = FALSE;
if(! tipHomogeneityChecker(tr, q->back, 0))
doQ = FALSE;
if(doQ == FALSE && doP == FALSE)
return 0;
}
if((p->number > tr->mxtips) && doP)
{
p1 = p->next->back;
p2 = p->next->next->back;
if ((p1->number > tr->mxtips) || (p2->number > tr->mxtips))
{
removeNodeParsimony(p, tr);
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);
}
hookupDefault(p->next, p1, tr->numBranches);
hookupDefault(p->next->next, p2, tr->numBranches);
newviewParsimony(tr, p);
}
}
if ((q->number > tr->mxtips) && (maxtrav > 0) && doQ)
{
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, tr);
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);
}
hookupDefault(q->next, q1, tr->numBranches);
hookupDefault(q->next->next, q2, tr->numBranches);
newviewParsimony(tr, q);
}
}
return 1;
}
static void restoreTreeRearrangeParsimony(tree *tr)
{
removeNodeParsimony(tr->removeNode, tr);
restoreTreeParsimony(tr, tr->removeNode, tr->insertNode);
}
/*
static boolean isInformative2(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 boolean isInformative(tree *tr, int dataType, int site)
{
int
informativeCounter = 0,
check[256],
j,
undetermined = getUndetermined(dataType);
const unsigned int
*bitVector = getBitVector(dataType);
unsigned char
nucleotide;
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;
assert(bitVector[nucleotide] > 0);
}
for(j = 0; j < undetermined; j++)
{
if(check[j] > 0)
informativeCounter++;
}
if(informativeCounter <= 1)
return FALSE;
else
{
for(j = 0; j < undetermined; j++)
{
if(check[j] > 1)
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, tr->dataVector[i], 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;
}
}
assert(found != 0);
reorderNodes(tr, np, p->next->back, count);
reorderNodes(tr, np, p->next->next->back, count);
}
}
static void compressDNA(tree *tr, int *informative, boolean saveMemory)
{
size_t
totalNodes,
i,
model;
if(saveMemory)
totalNodes = (size_t)tr->innerNodes + 1 + (size_t)tr->mxtips;
else
totalNodes = 2 * (size_t)tr->mxtips;
for(model = 0; model < (size_t) tr->NumberOfModels; model++)
{
size_t
k,
states = (size_t)tr->partitionData[model].states,
compressedEntries,
compressedEntriesPadded,
entries = 0,
lower = tr->partitionData[model].lower,
upper = tr->partitionData[model].upper;
parsimonyNumber
**compressedTips = (parsimonyNumber **)rax_malloc(states * sizeof(parsimonyNumber*)),
*compressedValues = (parsimonyNumber *)rax_malloc(states * sizeof(parsimonyNumber));
for(i = lower; i < upper; i++)
if(informative[i])
entries += (size_t)tr->cdta->aliaswgt[i];
compressedEntries = entries / PCF;
if(entries % PCF != 0)
compressedEntries++;
#if (defined(__SIM_SSE3) || defined(__AVX))
if(compressedEntries % INTS_PER_VECTOR != 0)
compressedEntriesPadded = compressedEntries + (INTS_PER_VECTOR - (compressedEntries % INTS_PER_VECTOR));
else
compressedEntriesPadded = compressedEntries;
#else
compressedEntriesPadded = compressedEntries;
#endif
tr->partitionData[model].parsVect = (parsimonyNumber *)rax_malloc((size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber));
for(i = 0; i < compressedEntriesPadded * states * totalNodes; i++)
tr->partitionData[model].parsVect[i] = 0;
for(i = 0; i < (size_t)tr->mxtips; i++)
{
size_t
w = 0,
compressedIndex = 0,
compressedCounter = 0,
index = 0;
for(k = 0; k < states; k++)
{
compressedTips[k] = &(tr->partitionData[model].parsVect[(compressedEntriesPadded * states * (i + 1)) + (compressedEntriesPadded * k)]);
compressedValues[k] = 0;
}
for(index = lower; index < (size_t)upper; index++)
{
if(informative[index])
{
const unsigned int
*bitValue = getBitVector(tr->partitionData[model].dataType);
parsimonyNumber
value = bitValue[tr->yVector[i + 1][index]];
for(w = 0; w < (size_t)tr->cdta->aliaswgt[index]; w++)
{
for(k = 0; k < states; k++)
{
if(value & mask32[k])
compressedValues[k] |= mask32[compressedCounter];
}
compressedCounter++;
if(compressedCounter == PCF)
{
for(k = 0; k < states; k++)
{
compressedTips[k][compressedIndex] = compressedValues[k];
compressedValues[k] = 0;
}
compressedCounter = 0;
compressedIndex++;
}
}
}
}
for(;compressedIndex < compressedEntriesPadded; compressedIndex++)
{
for(;compressedCounter < PCF; compressedCounter++)
for(k = 0; k < states; k++)
compressedValues[k] |= mask32[compressedCounter];
for(k = 0; k < states; k++)
{
compressedTips[k][compressedIndex] = compressedValues[k];
compressedValues[k] = 0;
}
compressedCounter = 0;
}
}
tr->partitionData[model].parsimonyLength = compressedEntriesPadded;
rax_free(compressedTips);
rax_free(compressedValues);
}
tr->parsimonyScore = (unsigned int*)rax_malloc(sizeof(unsigned int) * totalNodes);
for(i = 0; i < totalNodes; i++)
tr->parsimonyScore[i] = 0;
}
static void stepwiseAddition(tree *tr, nodeptr p, nodeptr q)
{
nodeptr
r = q->back;
unsigned int
mp;
int
counter = 4;
p->next->back = q;
q->back = p->next;
p->next->next->back = r;
r->back = p->next->next;
computeTraversalInfoParsimony(p, tr->ti, &counter, tr->mxtips, FALSE);
tr->ti[0] = counter;
tr->ti[1] = p->number;
tr->ti[2] = p->back->number;
mp = evaluateParsimonyIterativeFast(tr);
if(mp < tr->bestParsimony)
{
tr->bestParsimony = mp;
tr->insertNode = q;
}
q->back = r;
r->back = q;
if(q->number > tr->mxtips && tr->parsimonyScore[q->number] > 0)
{
stepwiseAddition(tr, p, q->next->back);
stepwiseAddition(tr, p, q->next->next->back);
}
}
static void markNodesInTree(nodeptr p, tree *tr, unsigned char *nodesInTree)
{
if(isTip(p->number, tr->mxtips))
nodesInTree[p->number] = 1;
else
{
markNodesInTree(p->next->back, tr, nodesInTree);
markNodesInTree(p->next->next->back, tr, nodesInTree);
}
}
void makeParsimonyTreeFast(tree *tr, analdef *adef, boolean full)
{
nodeptr
p,
f;
size_t
model;
int
i,
nextsp,
*perm = (int *)rax_malloc((size_t)(tr->mxtips + 1) * sizeof(int)),
*informative = (int *)rax_malloc(sizeof(int) * (size_t)tr->cdta->endsite);
unsigned int
randomMP,
startMP;
/* double t; */
determineUninformativeSites(tr, informative);
compressDNA(tr, informative, FALSE);
rax_free(informative);
tr->ti = (int*)rax_malloc(sizeof(int) * 4 * (size_t)tr->mxtips);
/*t = gettime();*/
if(!full)
{
int
j = 0;
unsigned char
*nodesInTree = (unsigned char*)rax_calloc((size_t)(tr->mxtips + 1), sizeof(unsigned char));
tr->start = findAnyTipFast(tr->start, tr->rdta->numsp);
tr->bestParsimony = INT_MAX;
evaluateParsimony(tr, tr->start->back, TRUE);
assert(tr->start);
checkSeed(adef);
markNodesInTree(tr->start, tr, nodesInTree);
markNodesInTree(tr->start->back, tr, nodesInTree);
j = tr->ntips + 1;
if(tr->grouped)
{
for(i = 1; i <= tr->mxtips; i++)
{
if(tr->constraintVector[i] == -1)
{
perm[j++] = i;
tr->constraintVector[i] = -9;
}
}
}
else
{
if(tr->constrained)
{
for(i = 1; i <= tr->mxtips; i++)
tr->constraintVector[i] = 0;
for(i = 1; i <= tr->mxtips; i++)
{
if(nodesInTree[i] == 0)
perm[j++] = i;
else
tr->constraintVector[i] = 1;
}
}
else
{
for(i = 1; i <= tr->mxtips; i++)
if(nodesInTree[i] == 0)
perm[j++] = i;
}
}
for(i = tr->ntips + 1; i <= tr->mxtips; i++)
{
int k, j;
k = (int)((double)(tr->mxtips + 1 - i) * randum(&adef->parsimonySeed));
assert(i + k <= tr->mxtips);
j = perm[i];
perm[i] = perm[i + k];
perm[i + k] = j;
}
f = tr->start;
rax_free(nodesInTree);
}
else
{
assert(!tr->constrained);
makePermutation(perm, 1, tr->mxtips, adef);
tr->ntips = 0;
tr->nextnode = tr->mxtips + 1;
buildSimpleTree(tr, perm[1], perm[2], perm[3]);
f = tr->start;
}
while(tr->ntips < tr->mxtips)
{
nodeptr q;
tr->bestParsimony = INT_MAX;
nextsp = ++(tr->ntips);
p = tr->nodep[perm[nextsp]];
q = tr->nodep[(tr->nextnode)++];
p->back = q;
q->back = p;
if(tr->grouped && !full)
{
int
number = p->back->number;
tr->constraintVector[number] = -9;
}
stepwiseAddition(tr, q, f->back);
{
nodeptr
r = tr->insertNode->back;
int counter = 4;
hookupDefault(q->next, tr->insertNode, tr->numBranches);
hookupDefault(q->next->next, r, tr->numBranches);
computeTraversalInfoParsimony(q, tr->ti, &counter, tr->mxtips, FALSE);
tr->ti[0] = counter;
newviewParsimonyIterativeFast(tr);
}
}
//printf("ADD: %d\n", tr->bestParsimony);
nodeRectifier(tr);
if(adef->stepwiseAdditionOnly == FALSE)
{
randomMP = tr->bestParsimony;
do
{
startMP = randomMP;
nodeRectifier(tr);
for(i = 1; i <= tr->mxtips + tr->mxtips - 2; i++)
{
rearrangeParsimony(tr, tr->nodep[i], 1, 20, FALSE);
if(tr->bestParsimony < randomMP)
{
restoreTreeRearrangeParsimony(tr);
randomMP = tr->bestParsimony;
}
}
}
while(randomMP < startMP);
}
//printf("OPT: %d\n", tr->bestParsimony);
rax_free(perm);
rax_free(tr->parsimonyScore);
for(model = 0; model < (size_t) tr->NumberOfModels; model++)
rax_free(tr->partitionData[model].parsVect);
rax_free(tr->ti);
}
static void insertRandom (nodeptr p, nodeptr q, int numBranches)
{
nodeptr r;
r = q->back;
hookupDefault(p->next, q, numBranches);
hookupDefault(p->next->next, r, numBranches);
}
static void buildSimpleTreeRandom (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];
hookupDefault(p, tr->nodep[iq], tr->numBranches);
s = buildNewTip(tr, tr->nodep[ir]);
insertRandom(s, p, tr->numBranches);
}
int checker(tree *tr, nodeptr p)
{
int group = tr->constraintVector[p->number];
if(isTip(p->number, tr->mxtips))
{
group = tr->constraintVector[p->number];
return group;
}
else
{
if(group != -9)
return group;
group = checker(tr, p->next->back);
if(group != -9)
return group;
group = checker(tr, p->next->next->back);
if(group != -9)
return group;
return -9;
}
}
static int markBranches(nodeptr *branches, nodeptr p, int *counter, int numsp)
{
if(isTip(p->number, numsp))
return 0;
else
{
branches[*counter] = p->next;
branches[*counter + 1] = p->next->next;
*counter = *counter + 2;
return ((2 + markBranches(branches, p->next->back, counter, numsp) +
markBranches(branches, p->next->next->back, counter, numsp)));
}
}
nodeptr findAnyTip(nodeptr p, int numsp)
{
return isTip(p->number, numsp) ? p : findAnyTip(p->next->back, numsp);
}
int randomInt(int n, analdef *adef)
{
return ((int)(randum(&adef->parsimonySeed) * (double)n));
// return rand() %n;
}
void makePermutation(int *perm, int lower, int n, analdef *adef)
{
int i, j, k;
checkSeed(adef);
for (i = lower; i <= n; i++)
perm[i] = i;
for (i = lower; i <= n; i++)
{
k = (int)((double)(n + 1 - i) * randum(&adef->parsimonySeed));
assert(i + k <= n);
j = perm[i];
perm[i] = perm[i + k];
perm[i + k] = j;
}
}
boolean tipHomogeneityChecker(tree *tr, nodeptr p, int grouping)
{
if(isTip(p->number, tr->mxtips))
{
if(tr->constraintVector[p->number] != grouping)
return FALSE;
else
return TRUE;
}
else
{
return (tipHomogeneityChecker(tr, p->next->back, grouping) && tipHomogeneityChecker(tr, p->next->next->back,grouping));
}
}
void makeRandomTree(tree *tr, analdef *adef)
{
nodeptr p, f, randomBranch;
int nextsp;
int *perm, branchCounter;
nodeptr *branches;
branches = (nodeptr *)rax_malloc(sizeof(nodeptr) * (2 * tr->mxtips));
perm = (int *)rax_malloc((tr->mxtips + 1) * sizeof(int));
makePermutation(perm, 1, tr->mxtips, adef);
tr->ntips = 0;
tr->nextnode = tr->mxtips + 1;
buildSimpleTreeRandom(tr, perm[1], perm[2], perm[3]);
while (tr->ntips < tr->mxtips)
{
tr->bestParsimony = INT_MAX;
nextsp = ++(tr->ntips);
p = tr->nodep[perm[nextsp]];
/*printf("ADDING SPECIES %d\n", nextsp);*/
buildNewTip(tr, p);
f = findAnyTip(tr->start, tr->mxtips);
f = f->back;
branchCounter = 1;
branches[0] = f;
markBranches(branches, f, &branchCounter, tr->mxtips);
assert(branchCounter == ((2 * (tr->ntips - 1)) - 3));
randomBranch = branches[randomInt(branchCounter, adef)];
insertRandom(p->back, randomBranch, tr->numBranches);
}
rax_free(perm);
rax_free(branches);
}
void nodeRectifier(tree *tr)
{
nodeptr *np = (nodeptr *)rax_malloc(2 * tr->mxtips * sizeof(nodeptr));
int i;
int count = 0;
tr->start = tr->nodep[1];
tr->rooted = FALSE;
/* TODO why is tr->rooted set to FALSE here ?*/
for(i = tr->mxtips + 1; i <= (tr->mxtips + tr->mxtips - 1); i++)
np[i] = tr->nodep[i];
reorderNodes(tr, np, tr->start->back, &count);
rax_free(np);
}
void makeParsimonyTree(tree *tr, analdef *adef)
{
makeParsimonyTreeFast(tr, adef, TRUE);
}
void makeParsimonyTreeIncomplete(tree *tr, analdef *adef)
{
makeParsimonyTreeFast(tr, adef, FALSE);
}
static void setupBranchMetaInfo(tree *tr, nodeptr p, int nTips, branchInfo *bInf)
{
int
countBranches = tr->branchCounter;
if(isTip(p->number, tr->mxtips))
{
p->bInf = &bInf[countBranches];
p->back->bInf = &bInf[countBranches];
bInf[countBranches].oP = p;
bInf[countBranches].oQ = p->back;
bInf[countBranches].epa->leftNodeNumber = p->number;
bInf[countBranches].epa->rightNodeNumber = p->back->number;
bInf[countBranches].epa->branchNumber = countBranches;
bInf[countBranches].epa->originalBranchLength = p->z[0];
tr->branchCounter = tr->branchCounter + 1;
return;
}
else
{
nodeptr q;
assert(p == p->next->next->next);
p->bInf = &bInf[countBranches];
p->back->bInf = &bInf[countBranches];
bInf[countBranches].oP = p;
bInf[countBranches].oQ = p->back;
bInf[countBranches].epa->leftNodeNumber = p->number;
bInf[countBranches].epa->rightNodeNumber = p->back->number;
bInf[countBranches].epa->branchNumber = countBranches;
bInf[countBranches].epa->originalBranchLength = p->z[0];
tr->branchCounter = tr->branchCounter + 1;
q = p->next;
while(q != p)
{
setupBranchMetaInfo(tr, q->back, nTips, bInf);
q = q->next;
}
return;
}
}
static void setupJointFormat(tree *tr, nodeptr p, int ntips, branchInfo *bInf, int *count)
{
if(isTip(p->number, tr->mxtips))
{
p->bInf->epa->jointLabel = *count;
*count = *count + 1;
return;
}
else
{
setupJointFormat(tr, p->next->back, ntips, bInf, count);
setupJointFormat(tr, p->next->next->back, ntips, bInf, count);
p->bInf->epa->jointLabel = *count;
*count = *count + 1;
return;
}
}
static void setupBranchInfo(tree *tr, nodeptr q)
{
nodeptr
originalNode = tr->nodep[tr->mxtips + 1];
int
count = 0;
tr->branchCounter = 0;
setupBranchMetaInfo(tr, q, tr->ntips, tr->bInf);
assert(tr->branchCounter == tr->numberOfBranches);
if(tr->wasRooted)
{
assert(tr->leftRootNode->back == tr->rightRootNode);
assert(tr->leftRootNode == tr->rightRootNode->back);
if(!isTip(tr->leftRootNode->number, tr->mxtips))
{
setupJointFormat(tr, tr->leftRootNode->next->back, tr->ntips, tr->bInf, &count);
setupJointFormat(tr, tr->leftRootNode->next->next->back, tr->ntips, tr->bInf, &count);
}
tr->leftRootNode->bInf->epa->jointLabel = count;
tr->rootLabel = count;
count = count + 1;
if(!isTip(tr->rightRootNode->number, tr->mxtips))
{
setupJointFormat(tr, tr->rightRootNode->next->back, tr->ntips, tr->bInf, &count);
setupJointFormat(tr, tr->rightRootNode->next->next->back, tr->ntips, tr->bInf, &count);
}
}
else
{
setupJointFormat(tr, originalNode->back, tr->ntips, tr->bInf, &count);
setupJointFormat(tr, originalNode->next->back, tr->ntips, tr->bInf, &count);
setupJointFormat(tr, originalNode->next->next->back, tr->ntips, tr->bInf, &count);
}
assert(count == tr->numberOfBranches);
}
static void testInsertFast(tree *tr, nodeptr r, nodeptr q)
{
unsigned int
result;
nodeptr
x = q->back;
int
i,
*inserts = tr->inserts;
assert(!tr->grouped);
hookupDefault(r->next, q, tr->numBranches);
hookupDefault(r->next->next, x, tr->numBranches);
newviewParsimony(tr, r);
for(i = 0; i < tr->numberOfTipsForInsertion; i++)
{
hookupDefault(r, tr->nodep[inserts[i]], tr->numBranches);
tr->bestParsimony = INT_MAX;
result = evaluateParsimony(tr, r, FALSE);
r->back = (nodeptr) NULL;
tr->nodep[inserts[i]]->back = (nodeptr) NULL;
tr->bInf[q->bInf->epa->branchNumber].epa->parsimonyScore[i] = result;
}
hookupDefault(q, x, tr->numBranches);
r->next->next->back = r->next->back = (nodeptr) NULL;
}
static void traverseTree(tree *tr, nodeptr r, nodeptr q)
{
testInsertFast(tr, r, q);
if(!isTip(q->number, tr->rdta->numsp))
{
nodeptr
a = q->next;
while(a != q)
{
traverseTree(tr, r, a->back);
a = a->next;
}
}
}
typedef struct
{
unsigned int parsimonyScore;
int number;
}
infoMP;
static int infoCompare(const void *p1, const void *p2)
{
infoMP *rc1 = (infoMP *)p1;
infoMP *rc2 = (infoMP *)p2;
unsigned int i = rc1->parsimonyScore;
unsigned int j = rc2->parsimonyScore;
if (i > j)
return (1);
if (i < j)
return (-1);
return (0);
}
void classifyMP(tree *tr, analdef *adef)
{
int
*informative = (int *)rax_malloc(sizeof(int) * (size_t)tr->cdta->endsite),
i,
j,
*perm;
infoMP
*inf;
nodeptr
r,
q;
char
jointFormatTreeFileName[1024],
originalLabelledTreeFileName[1024],
labelledTreeFileName[1024],
likelihoodWeightsFileName[1024];
FILE
*likelihoodWeightsFile,
*treeFile;
unsigned int
score;
assert(adef->restart);
determineUninformativeSites(tr, informative);
compressDNA(tr, informative, TRUE);
rax_free(informative);
tr->ti = (int*)rax_malloc(sizeof(int) * 4 * (size_t)tr->mxtips);
tr->numberOfBranches = 2 * tr->ntips - 3;
printBothOpen("\nRAxML Evolutionary Placement Algorithm using parsimony\n");
tr->bestParsimony = INT_MAX;
score = evaluateParsimony(tr, tr->start->back, TRUE);
printBothOpen("\nparsimony score of reference tree: %u\n\n", score);
perm = (int *)rax_calloc(((size_t)tr->mxtips) + 1, sizeof(int));
tr->inserts = (int *)rax_calloc((size_t)tr->mxtips, sizeof(int));
markTips(tr->start, perm, tr->mxtips);
markTips(tr->start->back, perm ,tr->mxtips);
tr->numberOfTipsForInsertion = 0;
for(i = 1; i <= tr->mxtips; i++)
{
if(perm[i] == 0)
{
tr->inserts[tr->numberOfTipsForInsertion] = i;
tr->numberOfTipsForInsertion = tr->numberOfTipsForInsertion + 1;
}
}
rax_free(perm);
printBothOpen("RAxML will place %d Query Sequences into the %d branches of the reference tree with %d taxa\n\n", tr->numberOfTipsForInsertion, (2 * tr->ntips - 3), tr->ntips);
assert(tr->numberOfTipsForInsertion == (tr->mxtips - tr->ntips));
tr->bInf = (branchInfo*)rax_malloc(tr->numberOfBranches * sizeof(branchInfo));
for(i = 0; i < tr->numberOfBranches; i++)
{
tr->bInf[i].epa = (epaBranchData*)rax_malloc(sizeof(epaBranchData));
tr->bInf[i].epa->parsimonyScore = (unsigned int*)rax_malloc(tr->numberOfTipsForInsertion * sizeof(unsigned int));
for(j = 0; j < tr->numberOfTipsForInsertion; j++)
tr->bInf[i].epa->parsimonyScore[j] = INT_MAX;
tr->bInf[i].epa->branchNumber = i;
tr->bInf[i].epa->countThem = (int*)rax_calloc(tr->numberOfTipsForInsertion, sizeof(int));
sprintf(tr->bInf[i].epa->branchLabel, "I%d", i);
}
r = tr->nodep[(tr->nextnode)++];
q = findAnyTip(tr->start, tr->rdta->numsp);
assert(isTip(q->number, tr->rdta->numsp));
assert(!isTip(q->back->number, tr->rdta->numsp));
q = q->back;
setupBranchInfo(tr, q);
traverseTree(tr, r, q);
printBothOpen("Overall Classification time: %f\n\n", gettime() - masterTime);
strcpy(jointFormatTreeFileName, workdir);
strcpy(originalLabelledTreeFileName, workdir);
strcpy(labelledTreeFileName, workdir);
strcpy(likelihoodWeightsFileName, workdir);
strcat(jointFormatTreeFileName, "RAxML_portableTree.");
strcat(originalLabelledTreeFileName, "RAxML_originalLabelledTree.");
strcat(labelledTreeFileName, "RAxML_labelledTree.");
strcat(likelihoodWeightsFileName, "RAxML_equallyParsimoniousPlacements.");
strcat(jointFormatTreeFileName, run_id);
strcat(originalLabelledTreeFileName, run_id);
strcat(labelledTreeFileName, run_id);
strcat(likelihoodWeightsFileName, run_id);
strcat(jointFormatTreeFileName, ".jplace");
rax_free(tr->tree_string);
tr->treeStringLength *= 16;
tr->tree_string = (char*)rax_calloc(tr->treeStringLength, sizeof(char));
treeFile = myfopen(originalLabelledTreeFileName, "wb");
Tree2StringClassify(tr->tree_string, tr, tr->inserts, TRUE, FALSE, FALSE, tr->mxtips + 1, FALSE);
fprintf(treeFile, "%s\n", tr->tree_string);
fclose(treeFile);
treeFile = myfopen(jointFormatTreeFileName, "wb");
Tree2StringClassify(tr->tree_string, tr, tr->inserts, TRUE, TRUE, FALSE, tr->mxtips + 1, FALSE);
fprintf(treeFile, "{\n");
fprintf(treeFile, "\t\"tree\": \"%s\", \n", tr->tree_string);
fprintf(treeFile, "\t\"placements\": [\n");
inf = (infoMP*)rax_malloc(sizeof(infoMP) * tr->numberOfBranches);
/* joint format */
for(i = 0; i < tr->numberOfTipsForInsertion; i++)
{
unsigned int
lmax;
int
validEntries = tr->numberOfBranches;
for(j = 0; j < tr->numberOfBranches; j++)
{
inf[j].parsimonyScore = tr->bInf[j].epa->parsimonyScore[i];
inf[j].number = tr->bInf[j].epa->jointLabel;
}
qsort(inf, tr->numberOfBranches, sizeof(infoMP), infoCompare);
j = 0;
lmax = inf[0].parsimonyScore;
fprintf(treeFile, "\t{\"p\":[");
while(j < validEntries && inf[j].parsimonyScore == lmax)
{
if(j > 0)
{
if(tr->wasRooted && inf[j].number == tr->rootLabel)
assert(0);
else
fprintf(treeFile, ",[%d, %u]", inf[j].number, inf[j].parsimonyScore);
}
else
{
if(tr->wasRooted && inf[j].number == tr->rootLabel)
assert(0);
else
fprintf(treeFile, "[%d, %u]", inf[j].number, inf[j].parsimonyScore);
}
j++;
}
if(i == tr->numberOfTipsForInsertion - 1)
fprintf(treeFile, "], \"n\":[\"%s\"]}\n", tr->nameList[tr->inserts[i]]);
else
fprintf(treeFile, "], \"n\":[\"%s\"]},\n", tr->nameList[tr->inserts[i]]);
}
fprintf(treeFile, "\t ],\n");
/* fprintf(treeFile, "\t\"metadata\": {\"invocation\": \"RAxML EPA parsimony\"},\n");*/
fprintf(treeFile, "\t\"metadata\": {\"invocation\": ");
fprintf(treeFile, "\"");
{
int i;
for(i = 0; i < globalArgc; i++)
fprintf(treeFile,"%s ", globalArgv[i]);
}
fprintf(treeFile, "\", \"raxml_version\": \"%s\"", programVersion);
fprintf(treeFile,"},\n");
fprintf(treeFile, "\t\"version\": 2,\n");
fprintf(treeFile, "\t\"fields\": [\n");
fprintf(treeFile, "\t\"edge_num\", \"parsimony\"\n");
fprintf(treeFile, "\t]\n");
fprintf(treeFile, "}\n");
fclose(treeFile);
/* JSON format end */
likelihoodWeightsFile = myfopen(likelihoodWeightsFileName, "wb");
for(i = 0; i < tr->numberOfTipsForInsertion; i++)
{
unsigned int
lmax;
int
validEntries = tr->numberOfBranches;
for(j = 0; j < tr->numberOfBranches; j++)
{
inf[j].parsimonyScore = tr->bInf[j].epa->parsimonyScore[i];
inf[j].number = j;
}
qsort(inf, tr->numberOfBranches, sizeof(infoMP), infoCompare);
j = 0;
lmax = inf[0].parsimonyScore;
while(j < validEntries && inf[j].parsimonyScore == lmax)
{
fprintf(likelihoodWeightsFile, "%s I%d %u\n", tr->nameList[tr->inserts[i]], inf[j].number, inf[j].parsimonyScore);
tr->bInf[inf[j].number].epa->countThem[i] = 1;
j++;
}
}
rax_free(inf);
fclose(likelihoodWeightsFile);
Tree2StringClassify(tr->tree_string, tr, tr->inserts, FALSE, FALSE, FALSE, tr->mxtips + 1, FALSE);
treeFile = fopen(labelledTreeFileName, "wb");
fprintf(treeFile, "%s\n", tr->tree_string);
fclose(treeFile);
printBothOpen("Equally parsimonious read placements written to file: %s\n\n", likelihoodWeightsFileName);
printBothOpen("Labelled reference tree with branch labels (without query sequences) written to file: %s\n\n", originalLabelledTreeFileName);
printBothOpen("Labelled reference tree with branch labels in portable pplacer/EPA format (without query sequences) written to file: %s\n\n", jointFormatTreeFileName);
printBothOpen("Labelled reference tree including branch labels and query sequences written to file: %s\n\n", labelledTreeFileName);
exit(0);
}
#ifdef __AVX
#ifdef _SSE3_WAS_DEFINED
#define __SIM_SSE3
#undef _SSE3_WAS_DEFINED
#endif
#endif