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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 <math.h>
#include <time.h>
#include <stdlib.h>
#include <stdio.h>
#include <ctype.h>
#include <string.h>
#include "axml.h"
extern int Thorough;
extern infoList iList;
extern char seq_file[1024];
extern char resultFileName[1024];
extern char tree_file[1024];
extern char workdir[1024];
extern char run_id[128];
extern FILE *INFILE;
extern double masterTime;
boolean initrav (tree *tr, nodeptr p)
{
nodeptr q;
if (!isTip(p->number, tr->rdta->numsp))
{
q = p->next;
do
{
if (! initrav(tr, q->back)) return FALSE;
q = q->next;
}
while (q != p);
newviewGeneric(tr, p);
}
return TRUE;
}
//#define _DEBUG_UPDATE
boolean update(tree *tr, nodeptr p)
{
nodeptr q;
boolean smoothedPartitions[NUM_BRANCHES];
int i;
double z[NUM_BRANCHES], z0[NUM_BRANCHES];
double _deltaz;
#ifdef _DEBUG_UPDATE
double
startLH;
evaluateGeneric(tr, p);
startLH = tr->likelihood;
#endif
q = p->back;
for(i = 0; i < tr->numBranches; i++)
z0[i] = q->z[i];
if(tr->numBranches > 1)
makenewzGeneric(tr, p, q, z0, newzpercycle, z, TRUE);
else
makenewzGeneric(tr, p, q, z0, newzpercycle, z, FALSE);
for(i = 0; i < tr->numBranches; i++)
smoothedPartitions[i] = tr->partitionSmoothed[i];
for(i = 0; i < tr->numBranches; i++)
{
if(!tr->partitionConverged[i])
{
_deltaz = deltaz;
if(ABS(z[i] - z0[i]) > _deltaz)
{
/*
#ifdef _DEBUG_UPDATE
printf("accept\n");
#endif
*/
smoothedPartitions[i] = FALSE;
}
/*
#ifdef _DEBUG_UPDATE
else
printf("reject\n");
#endif
*/
p->z[i] = q->z[i] = z[i];
#ifdef _BASTIEN
//printf("update %f\n", tr->secondDerivative[i]);
p->secondDerivative[i] = q->secondDerivative[i] = tr->secondDerivative[i];
p->secondDerivativeValid[i] = q->secondDerivativeValid[i] = TRUE;
#endif
}
}
#ifdef _DEBUG_UPDATE
evaluateGeneric(tr, p);
if(tr->likelihood <= startLH)
{
if(fabs(tr->likelihood - startLH) > 0.01)
{
printf("%f %f\n", startLH, tr->likelihood);
assert(0);
}
}
#endif
for(i = 0; i < tr->numBranches; i++)
tr->partitionSmoothed[i] = smoothedPartitions[i];
return TRUE;
}
boolean smooth (tree *tr, nodeptr p)
{
nodeptr q;
if (! update(tr, p)) return FALSE; /* Adjust branch */
if (! isTip(p->number, tr->rdta->numsp))
{ /* Adjust descendants */
q = p->next;
while (q != p)
{
if (! smooth(tr, q->back)) return FALSE;
q = q->next;
}
if(tr->multiBranch)
newviewGenericMasked(tr, p);
else
newviewGeneric(tr, p);
}
return TRUE;
}
static boolean allSmoothed(tree *tr)
{
int i;
boolean result = TRUE;
for(i = 0; i < tr->numBranches; i++)
{
if(tr->partitionSmoothed[i] == FALSE)
result = FALSE;
else
tr->partitionConverged[i] = TRUE;
}
return result;
}
boolean smoothTree (tree *tr, int maxtimes)
{
nodeptr p, q;
int i, count = 0;
p = tr->start;
for(i = 0; i < tr->numBranches; i++)
tr->partitionConverged[i] = FALSE;
while (--maxtimes >= 0)
{
for(i = 0; i < tr->numBranches; i++)
tr->partitionSmoothed[i] = TRUE;
if (! smooth(tr, p->back)) return FALSE;
if (!isTip(p->number, tr->rdta->numsp))
{
q = p->next;
while (q != p)
{
if (! smooth(tr, q->back)) return FALSE;
q = q->next;
}
}
count++;
if (allSmoothed(tr))
break;
}
for(i = 0; i < tr->numBranches; i++)
tr->partitionConverged[i] = FALSE;
return TRUE;
}
boolean localSmooth (tree *tr, nodeptr p, int maxtimes)
{
nodeptr q;
int i;
if (isTip(p->number, tr->rdta->numsp)) return FALSE;
for(i = 0; i < tr->numBranches; i++)
tr->partitionConverged[i] = FALSE;
while (--maxtimes >= 0)
{
for(i = 0; i < tr->numBranches; i++)
tr->partitionSmoothed[i] = TRUE;
q = p;
do
{
if (! update(tr, q)) return FALSE;
q = q->next;
}
while (q != p);
if (allSmoothed(tr))
break;
}
for(i = 0; i < tr->numBranches; i++)
{
tr->partitionSmoothed[i] = FALSE;
tr->partitionConverged[i] = FALSE;
}
return TRUE;
}
static void resetInfoList(void)
{
int i;
iList.valid = 0;
for(i = 0; i < iList.n; i++)
{
iList.list[i].node = (nodeptr)NULL;
iList.list[i].likelihood = unlikely;
}
}
void initInfoList(int n)
{
int i;
iList.n = n;
iList.valid = 0;
iList.list = (bestInfo *)rax_malloc(sizeof(bestInfo) * n);
for(i = 0; i < n; i++)
{
iList.list[i].node = (nodeptr)NULL;
iList.list[i].likelihood = unlikely;
}
}
void freeInfoList(void)
{
rax_free(iList.list);
}
void insertInfoList(nodeptr node, double likelihood)
{
int i;
int min = 0;
double min_l = iList.list[0].likelihood;
for(i = 1; i < iList.n; i++)
{
if(iList.list[i].likelihood < min_l)
{
min = i;
min_l = iList.list[i].likelihood;
}
}
if(likelihood > min_l)
{
iList.list[min].likelihood = likelihood;
iList.list[min].node = node;
iList.valid += 1;
}
if(iList.valid > iList.n)
iList.valid = iList.n;
}
boolean smoothRegion (tree *tr, nodeptr p, int region)
{
nodeptr q;
if (! update(tr, p)) return FALSE; /* Adjust branch */
if(region > 0)
{
if (!isTip(p->number, tr->rdta->numsp))
{
q = p->next;
while (q != p)
{
if (! smoothRegion(tr, q->back, --region)) return FALSE;
q = q->next;
}
newviewGeneric(tr, p);
}
}
return TRUE;
}
boolean regionalSmooth (tree *tr, nodeptr p, int maxtimes, int region)
{
nodeptr q;
int i;
if (isTip(p->number, tr->rdta->numsp)) return FALSE; /* Should be an error */
for(i = 0; i < tr->numBranches; i++)
tr->partitionConverged[i] = FALSE;
while (--maxtimes >= 0)
{
for(i = 0; i < tr->numBranches; i++)
tr->partitionSmoothed[i] = TRUE;
q = p;
do
{
if (! smoothRegion(tr, q, region)) return FALSE;
q = q->next;
}
while (q != p);
if (allSmoothed(tr))
break;
}
for(i = 0; i < tr->numBranches; i++)
tr->partitionSmoothed[i] = FALSE;
for(i = 0; i < tr->numBranches; i++)
tr->partitionConverged[i] = FALSE;
return TRUE;
} /* localSmooth */
nodeptr removeNodeBIG (tree *tr, nodeptr p, int numBranches)
{
double zqr[NUM_BRANCHES], result[NUM_BRANCHES];
nodeptr q, r;
int i;
q = p->next->back;
r = p->next->next->back;
for(i = 0; i < numBranches; i++)
zqr[i] = q->z[i] * r->z[i];
makenewzGeneric(tr, q, r, zqr, iterations, result, FALSE);
for(i = 0; i < numBranches; i++)
tr->zqr[i] = result[i];
hookup(q, r, result, numBranches);
p->next->next->back = p->next->back = (node *) NULL;
return q;
}
nodeptr removeNodeRestoreBIG (tree *tr, nodeptr p)
{
nodeptr q, r;
q = p->next->back;
r = p->next->next->back;
newviewGeneric(tr, q);
newviewGeneric(tr, r);
hookup(q, r, tr->currentZQR, tr->numBranches);
p->next->next->back = p->next->back = (node *) NULL;
return q;
}
boolean insertBIG (tree *tr, nodeptr p, nodeptr q, int numBranches)
{
nodeptr r, s;
int i;
r = q->back;
s = p->back;
for(i = 0; i < numBranches; i++)
tr->lzi[i] = q->z[i];
#ifndef _HET
if(Thorough)
{
double zqr[NUM_BRANCHES], zqs[NUM_BRANCHES], zrs[NUM_BRANCHES], lzqr, lzqs, lzrs, lzsum, lzq, lzr, lzs, lzmax;
double defaultArray[NUM_BRANCHES];
double e1[NUM_BRANCHES], e2[NUM_BRANCHES], e3[NUM_BRANCHES];
double *qz;
qz = q->z;
for(i = 0; i < numBranches; i++)
defaultArray[i] = defaultz;
makenewzGeneric(tr, q, r, qz, iterations, zqr, FALSE);
makenewzGeneric(tr, q, s, defaultArray, iterations, zqs, FALSE);
makenewzGeneric(tr, r, s, defaultArray, iterations, zrs, FALSE);
for(i = 0; i < numBranches; i++)
{
lzqr = (zqr[i] > zmin) ? log(zqr[i]) : log(zmin);
lzqs = (zqs[i] > zmin) ? log(zqs[i]) : log(zmin);
lzrs = (zrs[i] > zmin) ? log(zrs[i]) : log(zmin);
lzsum = 0.5 * (lzqr + lzqs + lzrs);
lzq = lzsum - lzrs;
lzr = lzsum - lzqs;
lzs = lzsum - lzqr;
lzmax = log(zmax);
if (lzq > lzmax) {lzq = lzmax; lzr = lzqr; lzs = lzqs;}
else if (lzr > lzmax) {lzr = lzmax; lzq = lzqr; lzs = lzrs;}
else if (lzs > lzmax) {lzs = lzmax; lzq = lzqs; lzr = lzrs;}
e1[i] = exp(lzq);
e2[i] = exp(lzr);
e3[i] = exp(lzs);
}
hookup(p->next, q, e1, numBranches);
hookup(p->next->next, r, e2, numBranches);
hookup(p, s, e3, numBranches);
}
else
#endif
{
double z[NUM_BRANCHES];
for(i = 0; i < numBranches; i++)
{
z[i] = sqrt(q->z[i]);
if(z[i] < zmin)
z[i] = zmin;
if(z[i] > zmax)
z[i] = zmax;
}
hookup(p->next, q, z, tr->numBranches);
hookup(p->next->next, r, z, tr->numBranches);
}
newviewGeneric(tr, p);
if(Thorough)
{
localSmooth(tr, p, smoothings);
for(i = 0; i < numBranches; i++)
{
tr->lzq[i] = p->next->z[i];
tr->lzr[i] = p->next->next->z[i];
tr->lzs[i] = p->z[i];
}
}
return TRUE;
}
boolean insertRestoreBIG (tree *tr, nodeptr p, nodeptr q)
{
nodeptr r, s;
r = q->back;
s = p->back;
if(Thorough)
{
hookup(p->next, q, tr->currentLZQ, tr->numBranches);
hookup(p->next->next, r, tr->currentLZR, tr->numBranches);
hookup(p, s, tr->currentLZS, tr->numBranches);
}
else
{
double z[NUM_BRANCHES];
int i;
for(i = 0; i < tr->numBranches; i++)
{
double zz;
zz = sqrt(q->z[i]);
if(zz < zmin)
zz = zmin;
if(zz > zmax)
zz = zmax;
z[i] = zz;
}
hookup(p->next, q, z, tr->numBranches);
hookup(p->next->next, r, z, tr->numBranches);
}
newviewGeneric(tr, p);
return TRUE;
}
static void restoreTopologyOnly(tree *tr, bestlist *bt)
{
nodeptr p = tr->removeNode;
nodeptr q = tr->insertNode;
double qz[NUM_BRANCHES], pz[NUM_BRANCHES], p1z[NUM_BRANCHES], p2z[NUM_BRANCHES];
nodeptr p1, p2, r, s;
double currentLH = tr->likelihood;
int i;
p1 = p->next->back;
p2 = p->next->next->back;
for(i = 0; i < tr->numBranches; i++)
{
p1z[i] = p1->z[i];
p2z[i] = p2->z[i];
}
hookup(p1, p2, tr->currentZQR, tr->numBranches);
p->next->next->back = p->next->back = (node *) NULL;
for(i = 0; i < tr->numBranches; i++)
{
qz[i] = q->z[i];
pz[i] = p->z[i];
}
r = q->back;
s = p->back;
if(Thorough)
{
hookup(p->next, q, tr->currentLZQ, tr->numBranches);
hookup(p->next->next, r, tr->currentLZR, tr->numBranches);
hookup(p, s, tr->currentLZS, tr->numBranches);
}
else
{
double z[NUM_BRANCHES];
for(i = 0; i < tr->numBranches; i++)
{
z[i] = sqrt(q->z[i]);
if(z[i] < zmin)
z[i] = zmin;
if(z[i] > zmax)
z[i] = zmax;
}
hookup(p->next, q, z, tr->numBranches);
hookup(p->next->next, r, z, tr->numBranches);
}
tr->likelihood = tr->bestOfNode;
saveBestTree(bt, tr);
tr->likelihood = currentLH;
hookup(q, r, qz, tr->numBranches);
p->next->next->back = p->next->back = (nodeptr) NULL;
if(Thorough)
hookup(p, s, pz, tr->numBranches);
hookup(p->next, p1, p1z, tr->numBranches);
hookup(p->next->next, p2, p2z, tr->numBranches);
}
boolean testInsertBIG (tree *tr, nodeptr p, nodeptr q)
{
double qz[NUM_BRANCHES], pz[NUM_BRANCHES];
nodeptr r;
boolean doIt = TRUE;
double startLH = tr->endLH;
int i;
r = q->back;
for(i = 0; i < tr->numBranches; i++)
{
qz[i] = q->z[i];
pz[i] = p->z[i];
}
if(tr->grouped)
{
int rNumber, qNumber, pNumber;
doIt = FALSE;
rNumber = tr->constraintVector[r->number];
qNumber = tr->constraintVector[q->number];
pNumber = tr->constraintVector[p->number];
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)
{
if (! insertBIG(tr, p, q, tr->numBranches)) return FALSE;
evaluateGeneric(tr, p->next->next);
if(tr->likelihood > tr->bestOfNode)
{
tr->bestOfNode = tr->likelihood;
tr->insertNode = q;
tr->removeNode = p;
for(i = 0; i < tr->numBranches; i++)
{
tr->currentZQR[i] = tr->zqr[i];
tr->currentLZR[i] = tr->lzr[i];
tr->currentLZQ[i] = tr->lzq[i];
tr->currentLZS[i] = tr->lzs[i];
}
}
if(tr->likelihood > tr->endLH)
{
tr->insertNode = q;
tr->removeNode = p;
for(i = 0; i < tr->numBranches; i++)
tr->currentZQR[i] = tr->zqr[i];
tr->endLH = tr->likelihood;
}
hookup(q, r, qz, tr->numBranches);
p->next->next->back = p->next->back = (nodeptr) NULL;
if(Thorough)
{
nodeptr s = p->back;
hookup(p, s, pz, tr->numBranches);
}
if((tr->doCutoff) && (tr->likelihood < startLH))
{
tr->lhAVG += (startLH - tr->likelihood);
tr->lhDEC++;
if((startLH - tr->likelihood) >= tr->lhCutoff)
return FALSE;
else
return TRUE;
}
else
return TRUE;
}
else
return TRUE;
}
void addTraverseBIG(tree *tr, nodeptr p, nodeptr q, int mintrav, int maxtrav)
{
if (--mintrav <= 0)
{
if (! testInsertBIG(tr, p, q)) return;
}
if ((!isTip(q->number, tr->rdta->numsp)) && (--maxtrav > 0))
{
addTraverseBIG(tr, p, q->next->back, mintrav, maxtrav);
addTraverseBIG(tr, p, q->next->next->back, mintrav, maxtrav);
}
}
int rearrangeBIG(tree *tr, nodeptr p, int mintrav, int maxtrav)
{
double p1z[NUM_BRANCHES], p2z[NUM_BRANCHES], q1z[NUM_BRANCHES], q2z[NUM_BRANCHES];
nodeptr p1, p2, q, q1, q2;
int mintrav2, i;
boolean doP = TRUE, doQ = TRUE;
if (maxtrav < 1 || mintrav > maxtrav) 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 (!isTip(p->number, tr->rdta->numsp) && doP)
{
p1 = p->next->back;
p2 = p->next->next->back;
if(!isTip(p1->number, tr->rdta->numsp) || !isTip(p2->number, tr->rdta->numsp))
{
for(i = 0; i < tr->numBranches; i++)
{
p1z[i] = p1->z[i];
p2z[i] = p2->z[i];
}
if (! removeNodeBIG(tr, p, tr->numBranches)) return badRear;
if (!isTip(p1->number, tr->rdta->numsp))
{
addTraverseBIG(tr, p, p1->next->back,
mintrav, maxtrav);
addTraverseBIG(tr, p, p1->next->next->back,
mintrav, maxtrav);
}
if (!isTip(p2->number, tr->rdta->numsp))
{
addTraverseBIG(tr, p, p2->next->back,
mintrav, maxtrav);
addTraverseBIG(tr, p, p2->next->next->back,
mintrav, maxtrav);
}
hookup(p->next, p1, p1z, tr->numBranches);
hookup(p->next->next, p2, p2z, tr->numBranches);
newviewGeneric(tr, p);
}
}
if (!isTip(q->number, tr->rdta->numsp) && maxtrav > 0 && doQ)
{
q1 = q->next->back;
q2 = q->next->next->back;
/*if (((!q1->tip) && (!q1->next->back->tip || !q1->next->next->back->tip)) ||
((!q2->tip) && (!q2->next->back->tip || !q2->next->next->back->tip))) */
if (
(
! isTip(q1->number, tr->rdta->numsp) &&
(! isTip(q1->next->back->number, tr->rdta->numsp) || ! isTip(q1->next->next->back->number, tr->rdta->numsp))
)
||
(
! isTip(q2->number, tr->rdta->numsp) &&
(! isTip(q2->next->back->number, tr->rdta->numsp) || ! isTip(q2->next->next->back->number, tr->rdta->numsp))
)
)
{
for(i = 0; i < tr->numBranches; i++)
{
q1z[i] = q1->z[i];
q2z[i] = q2->z[i];
}
if (! removeNodeBIG(tr, q, tr->numBranches)) return badRear;
mintrav2 = mintrav > 2 ? mintrav : 2;
if (/*! q1->tip*/ !isTip(q1->number, tr->rdta->numsp))
{
addTraverseBIG(tr, q, q1->next->back,
mintrav2 , maxtrav);
addTraverseBIG(tr, q, q1->next->next->back,
mintrav2 , maxtrav);
}
if (/*! q2->tip*/ ! isTip(q2->number, tr->rdta->numsp))
{
addTraverseBIG(tr, q, q2->next->back,
mintrav2 , maxtrav);
addTraverseBIG(tr, q, q2->next->next->back,
mintrav2 , maxtrav);
}
hookup(q->next, q1, q1z, tr->numBranches);
hookup(q->next->next, q2, q2z, tr->numBranches);
newviewGeneric(tr, q);
}
}
return 1;
}
double treeOptimizeRapid(tree *tr, int mintrav, int maxtrav, analdef *adef, bestlist *bt)
{
int i, index,
*perm = (int*)NULL;
nodeRectifier(tr);
if (maxtrav > tr->ntips - 3)
maxtrav = tr->ntips - 3;
resetInfoList();
resetBestTree(bt);
tr->startLH = tr->endLH = tr->likelihood;
if(tr->doCutoff)
{
if(tr->bigCutoff)
{
if(tr->itCount == 0)
tr->lhCutoff = 0.5 * (tr->likelihood / -1000.0);
else
tr->lhCutoff = 0.5 * ((tr->lhAVG) / ((double)(tr->lhDEC)));
}
else
{
if(tr->itCount == 0)
tr->lhCutoff = tr->likelihood / -1000.0;
else
tr->lhCutoff = (tr->lhAVG) / ((double)(tr->lhDEC));
}
tr->itCount = tr->itCount + 1;
tr->lhAVG = 0;
tr->lhDEC = 0;
}
if(adef->permuteTreeoptimize)
{
int n = tr->mxtips + tr->mxtips - 2;
perm = (int *)rax_malloc(sizeof(int) * (n + 1));
makePermutation(perm, 1, n, adef);
}
for(i = 1; i <= tr->mxtips + tr->mxtips - 2; i++)
{
tr->bestOfNode = unlikely;
if(adef->permuteTreeoptimize)
index = perm[i];
else
index = i;
if(rearrangeBIG(tr, tr->nodep[index], mintrav, maxtrav))
{
if(Thorough)
{
if(tr->endLH > tr->startLH)
{
restoreTreeFast(tr);
tr->startLH = tr->endLH = tr->likelihood;
saveBestTree(bt, tr);
}
else
{
if(tr->bestOfNode != unlikely)
restoreTopologyOnly(tr, bt);
}
}
else
{
insertInfoList(tr->nodep[index], tr->bestOfNode);
if(tr->endLH > tr->startLH)
{
restoreTreeFast(tr);
tr->startLH = tr->endLH = tr->likelihood;
}
}
}
}
if(!Thorough)
{
Thorough = 1;
for(i = 0; i < iList.valid; i++)
{
tr->bestOfNode = unlikely;
if(rearrangeBIG(tr, iList.list[i].node, mintrav, maxtrav))
{
if(tr->endLH > tr->startLH)
{
restoreTreeFast(tr);
tr->startLH = tr->endLH = tr->likelihood;
saveBestTree(bt, tr);
}
else
{
if(tr->bestOfNode != unlikely)
{
restoreTopologyOnly(tr, bt);
}
}
}
}
Thorough = 0;
}
if(adef->permuteTreeoptimize)
rax_free(perm);
return tr->startLH;
}
boolean testInsertRestoreBIG (tree *tr, nodeptr p, nodeptr q)
{
if(Thorough)
{
if (! insertBIG(tr, p, q, tr->numBranches)) return FALSE;
evaluateGeneric(tr, p->next->next);
}
else
{
if (! insertRestoreBIG(tr, p, q)) return FALSE;
{
nodeptr x, y;
x = p->next->next;
y = p->back;
if(! isTip(x->number, tr->rdta->numsp) && isTip(y->number, tr->rdta->numsp))
{
while ((! x->x))
{
if (! (x->x))
newviewGeneric(tr, x);
}
}
if(isTip(x->number, tr->rdta->numsp) && !isTip(y->number, tr->rdta->numsp))
{
while ((! y->x))
{
if (! (y->x))
newviewGeneric(tr, y);
}
}
if(!isTip(x->number, tr->rdta->numsp) && !isTip(y->number, tr->rdta->numsp))
{
while ((! x->x) || (! y->x))
{
if (! (x->x))
newviewGeneric(tr, x);
if (! (y->x))
newviewGeneric(tr, y);
}
}
}
tr->likelihood = tr->endLH;
}
return TRUE;
}
void restoreTreeFast(tree *tr)
{
removeNodeRestoreBIG(tr, tr->removeNode);
testInsertRestoreBIG(tr, tr->removeNode, tr->insertNode);
}
//#define _DEBUG_RELL
static void updateRellTrees(tree *tr, int numberOfSamples)
{
int i, j;
#ifdef _DEBUG_RELL
int
impr = 0;
#endif
evaluateGenericVector(tr, tr->start);
for(i = 0; i < numberOfSamples; i++)
{
double
like = 0.0;
int
w = 0,
*weights = &(tr->resample[i * tr->originalCrunchedLength]);
for(j = 0; j < tr->originalCrunchedLength; j++)
{
w += weights[j];
like += (double)weights[j] * tr->perSiteLL[j];
}
if(like > tr->rellTrees->t[i]->likelihood)
{
#ifdef _DEBUG_RELL
impr = 1;
if(tr->rellTrees->t[i]->likelihood != unlikely)
printf("[%d] better tree found %f -> %f\n", i, tr->rellTrees->t[i]->likelihood, like);
else
printf("[%d] better tree found unlikely -> %f\n", i, like);
#endif
saveTreeList(tr->rellTrees, tr, i, like);
}
}
#ifdef _DEBUG_RELL
if(impr)
printf("\n\n");
#endif
}
int determineRearrangementSetting(tree *tr, analdef *adef, bestlist *bestT, bestlist *bt)
{
int i, mintrav, maxtrav, bestTrav, impr, index, MaxFast,
*perm = (int*)NULL;
double startLH;
boolean cutoff;
MaxFast = 26;
startLH = tr->likelihood;
cutoff = tr->doCutoff;
tr->doCutoff = FALSE;
mintrav = 1;
maxtrav = 5;
bestTrav = maxtrav = 5;
impr = 1;
resetBestTree(bt);
if(adef->permuteTreeoptimize)
{
int n = tr->mxtips + tr->mxtips - 2;
perm = (int *)rax_malloc(sizeof(int) * (n + 1));
makePermutation(perm, 1, n, adef);
}
while(impr && maxtrav < MaxFast)
{
recallBestTree(bestT, 1, tr);
nodeRectifier(tr);
if (maxtrav > tr->ntips - 3)
maxtrav = tr->ntips - 3;
tr->startLH = tr->endLH = tr->likelihood;
for(i = 1; i <= tr->mxtips + tr->mxtips - 2; i++)
{
if(adef->permuteTreeoptimize)
index = perm[i];
else
index = i;
tr->bestOfNode = unlikely;
if(rearrangeBIG(tr, tr->nodep[index], mintrav, maxtrav))
{
if(tr->endLH > tr->startLH)
{
restoreTreeFast(tr);
tr->startLH = tr->endLH = tr->likelihood;
}
}
}
treeEvaluate(tr, 0.25);
saveBestTree(bt, tr);
/*printf("DETERMINE_BEST: %d %f\n", maxtrav, tr->likelihood);*/
if(tr->likelihood > startLH)
{
startLH = tr->likelihood;
printLog(tr, adef, FALSE);
bestTrav = maxtrav;
impr = 1;
}
else
{
impr = 0;
}
maxtrav += 5;
if(tr->doCutoff)
{
tr->lhCutoff = (tr->lhAVG) / ((double)(tr->lhDEC));
tr->itCount = tr->itCount + 1;
tr->lhAVG = 0;
tr->lhDEC = 0;
}
}
recallBestTree(bt, 1, tr);
tr->doCutoff = cutoff;
if(adef->permuteTreeoptimize)
rax_free(perm);
return bestTrav;
}
/*
#define _TERRACES
define _TERRACES to better explore trees on terraces
*/
#ifdef _TERRACES
/* count the number of BS or ML tree search replicates */
int bCount = 0;
#endif
void computeBIGRAPID (tree *tr, analdef *adef, boolean estimateModel)
{
unsigned int
vLength = 0;
int
i,
impr,
bestTrav,
rearrangementsMax = 0,
rearrangementsMin = 0,
thoroughIterations = 0,
fastIterations = 0;
double lh, previousLh, difference, epsilon;
bestlist *bestT, *bt;
#ifdef _TERRACES
/* store the 20 best trees found in a dedicated list */
bestlist
*terrace;
/* output file names */
char
terraceFileName[1024],
buf[64];
#endif
hashtable *h = (hashtable*)NULL;
unsigned int **bitVectors = (unsigned int**)NULL;
if(tr->searchConvergenceCriterion)
{
bitVectors = initBitVector(tr, &vLength);
h = initHashTable(tr->mxtips * 4);
}
bestT = (bestlist *) rax_malloc(sizeof(bestlist));
bestT->ninit = 0;
initBestTree(bestT, 1, tr->mxtips);
bt = (bestlist *) rax_malloc(sizeof(bestlist));
bt->ninit = 0;
initBestTree(bt, 20, tr->mxtips);
#ifdef _TERRACES
/* initialize the tree list and the output file name for the current tree search/replicate */
terrace = (bestlist *) rax_malloc(sizeof(bestlist));
terrace->ninit = 0;
initBestTree(terrace, 20, tr->mxtips);
sprintf(buf, "%d", bCount);
strcpy(terraceFileName, workdir);
strcat(terraceFileName, "RAxML_terrace.");
strcat(terraceFileName, run_id);
strcat(terraceFileName, ".BS.");
strcat(terraceFileName, buf);
printf("%s\n", terraceFileName);
#endif
initInfoList(50);
difference = 10.0;
epsilon = 0.01;
Thorough = 0;
if(estimateModel)
{
if(adef->useBinaryModelFile)
{
readBinaryModel(tr, adef);
evaluateGenericInitrav(tr, tr->start);
treeEvaluate(tr, 2);
}
else
{
evaluateGenericInitrav(tr, tr->start);
modOpt(tr, adef, FALSE, 10.0);
}
}
else
treeEvaluate(tr, 2);
printLog(tr, adef, FALSE);
saveBestTree(bestT, tr);
if(!adef->initialSet)
bestTrav = adef->bestTrav = determineRearrangementSetting(tr, adef, bestT, bt);
else
bestTrav = adef->bestTrav = adef->initial;
if(estimateModel)
{
if(adef->useBinaryModelFile)
treeEvaluate(tr, 2);
else
{
evaluateGenericInitrav(tr, tr->start);
modOpt(tr, adef, FALSE, 5.0);
}
}
else
treeEvaluate(tr, 1);
saveBestTree(bestT, tr);
impr = 1;
if(tr->doCutoff)
tr->itCount = 0;
while(impr)
{
recallBestTree(bestT, 1, tr);
if(tr->searchConvergenceCriterion)
{
int bCounter = 0;
if(fastIterations > 1)
cleanupHashTable(h, (fastIterations % 2));
bitVectorInitravSpecial(bitVectors, tr->nodep[1]->back, tr->mxtips, vLength, h, fastIterations % 2, BIPARTITIONS_RF, (branchInfo *)NULL,
&bCounter, 1, FALSE, FALSE);
assert(bCounter == tr->mxtips - 3);
if(fastIterations > 0)
{
double rrf = convergenceCriterion(h, tr->mxtips);
if(rrf <= 0.01) /* 1% cutoff */
{
printBothOpen("ML fast search converged at fast SPR cycle %d with stopping criterion\n", fastIterations);
printBothOpen("Relative Robinson-Foulds (RF) distance between respective best trees after one succseful SPR cycle: %f%s\n", rrf, "%");
cleanupHashTable(h, 0);
cleanupHashTable(h, 1);
goto cleanup_fast;
}
else
printBothOpen("ML search convergence criterion fast cycle %d->%d Relative Robinson-Foulds %f\n", fastIterations - 1, fastIterations, rrf);
}
}
fastIterations++;
treeEvaluate(tr, 1.0);
saveBestTree(bestT, tr);
printLog(tr, adef, FALSE);
printResult(tr, adef, FALSE);
lh = previousLh = tr->likelihood;
treeOptimizeRapid(tr, 1, bestTrav, adef, bt);
impr = 0;
for(i = 1; i <= bt->nvalid; i++)
{
recallBestTree(bt, i, tr);
treeEvaluate(tr, 0.25);
if(adef->rellBootstrap)
updateRellTrees(tr, NUM_RELL_BOOTSTRAPS);
difference = ((tr->likelihood > previousLh)?
tr->likelihood - previousLh:
previousLh - tr->likelihood);
if(tr->likelihood > lh && difference > epsilon)
{
impr = 1;
lh = tr->likelihood;
saveBestTree(bestT, tr);
}
}
}
if(tr->searchConvergenceCriterion)
{
cleanupHashTable(h, 0);
cleanupHashTable(h, 1);
}
cleanup_fast:
Thorough = 1;
impr = 1;
recallBestTree(bestT, 1, tr);
if(estimateModel)
{
if(adef->useBinaryModelFile)
treeEvaluate(tr, 2);
else
{
evaluateGenericInitrav(tr, tr->start);
modOpt(tr, adef, FALSE, 1.0);
}
}
else
treeEvaluate(tr, 1.0);
while(1)
{
recallBestTree(bestT, 1, tr);
if(impr)
{
printResult(tr, adef, FALSE);
rearrangementsMin = 1;
rearrangementsMax = adef->stepwidth;
if(tr->searchConvergenceCriterion)
{
int bCounter = 0;
if(thoroughIterations > 1)
cleanupHashTable(h, (thoroughIterations % 2));
bitVectorInitravSpecial(bitVectors, tr->nodep[1]->back, tr->mxtips, vLength, h, thoroughIterations % 2, BIPARTITIONS_RF, (branchInfo *)NULL,
&bCounter, 1, FALSE, FALSE);
assert(bCounter == tr->mxtips - 3);
if(thoroughIterations > 0)
{
double rrf = convergenceCriterion(h, tr->mxtips);
if(rrf <= 0.01) /* 1% cutoff */
{
printBothOpen("ML search converged at thorough SPR cycle %d with stopping criterion\n", thoroughIterations);
printBothOpen("Relative Robinson-Foulds (RF) distance between respective best trees after one succseful SPR cycle: %f%s\n", rrf, "%");
goto cleanup;
}
else
printBothOpen("ML search convergence criterion thorough cycle %d->%d Relative Robinson-Foulds %f\n", thoroughIterations - 1, thoroughIterations, rrf);
}
}
thoroughIterations++;
}
else
{
rearrangementsMax += adef->stepwidth;
rearrangementsMin += adef->stepwidth;
if(rearrangementsMax > adef->max_rearrange)
goto cleanup;
}
treeEvaluate(tr, 1.0);
previousLh = lh = tr->likelihood;
saveBestTree(bestT, tr);
printLog(tr, adef, FALSE);
treeOptimizeRapid(tr, rearrangementsMin, rearrangementsMax, adef, bt);
impr = 0;
for(i = 1; i <= bt->nvalid; i++)
{
recallBestTree(bt, i, tr);
treeEvaluate(tr, 0.25);
if(adef->rellBootstrap)
updateRellTrees(tr, NUM_RELL_BOOTSTRAPS);
#ifdef _TERRACES
/* save all 20 best trees in the terrace tree list */
saveBestTree(terrace, tr);
#endif
difference = ((tr->likelihood > previousLh)?
tr->likelihood - previousLh:
previousLh - tr->likelihood);
if(tr->likelihood > lh && difference > epsilon)
{
impr = 1;
lh = tr->likelihood;
saveBestTree(bestT, tr);
}
}
}
cleanup:
#ifdef _TERRACES
{
double
bestLH = tr->likelihood;
FILE
*f = myfopen(terraceFileName, "w");
/* print out likelihood of best tree found */
printf("best tree: %f\n", tr->likelihood);
/* print out likelihoods of 20 best trees found during the tree search */
for(i = 1; i <= terrace->nvalid; i++)
{
recallBestTree(terrace, i, tr);
/* if the likelihood scores are smaller than some epsilon 0.000001
print the tree to file */
if(ABS(bestLH - tr->likelihood) < 0.000001)
{
printf("%d %f\n", i, tr->likelihood);
Tree2String(tr->tree_string, tr, tr->start->back, FALSE, TRUE, FALSE, FALSE, FALSE, adef, NO_BRANCHES, FALSE, FALSE, FALSE, FALSE);
fprintf(f, "%s\n", tr->tree_string);
}
}
fclose(f);
/* increment tree search counter */
bCount++;
}
#endif
if(tr->searchConvergenceCriterion)
{
freeBitVectors(bitVectors, 2 * tr->mxtips);
rax_free(bitVectors);
freeHashTable(h);
rax_free(h);
}
freeBestTree(bestT);
rax_free(bestT);
freeBestTree(bt);
rax_free(bt);
#ifdef _TERRACES
/* free terrace tree list */
freeBestTree(terrace);
rax_free(terrace);
#endif
freeInfoList();
printLog(tr, adef, FALSE);
printResult(tr, adef, FALSE);
}
boolean treeEvaluate (tree *tr, double smoothFactor) /* Evaluate a user tree */
{
boolean result;
if(tr->useBrLenScaler)
assert(0);
result = smoothTree(tr, (int)((double)smoothings * smoothFactor));
assert(result);
evaluateGeneric(tr, tr->start);
return TRUE;
}
static void setupBranches(tree *tr, nodeptr p, 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;
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;
tr->branchCounter = tr->branchCounter + 1;
q = p->next;
while(q != p)
{
setupBranches(tr, q->back, bInf);
q = q->next;
}
return;
}
}
static void smoothTreeRandom (tree *tr, int maxtimes, analdef *adef)
{
int i, k, *perm;
tr->branchCounter = 0;
tr->numberOfBranches = 2 * tr->mxtips - 3;
tr->bInf = (branchInfo*)rax_malloc(tr->numberOfBranches * sizeof(branchInfo));
perm = (int*)rax_malloc(sizeof(int) * tr->numberOfBranches);
setupBranches(tr, tr->start->back, tr->bInf);
for(i = 0; i < tr->numBranches; i++)
tr->partitionConverged[i] = FALSE;
/*printf("%d \n", maxtimes);*/
while (--maxtimes >= 0)
{
for(i = 0; i < tr->numBranches; i++)
tr->partitionSmoothed[i] = TRUE;
/*printf("%d %d\n", maxtimes, tr->numberOfBranches);*/
makePermutation(perm, 0, tr->numberOfBranches - 1, adef);
for(k = 0; k < tr->numberOfBranches; k++)
{
/*printf("%d Node %d\n", k, tr->bInf[k].oP->number);*/
update(tr, tr->bInf[perm[k]].oP);
newviewGeneric(tr, tr->bInf[perm[k]].oP);
}
/*if (! smooth(tr, p->back)) return FALSE;
if (!isTip(p->number, tr->rdta->numsp))
{
q = p->next;
while (q != p)
{
if (! smooth(tr, q->back)) return FALSE;
q = q->next;
}
}
*/
if (allSmoothed(tr))
break;
}
for(i = 0; i < tr->numBranches; i++)
tr->partitionConverged[i] = FALSE;
rax_free(tr->bInf);
rax_free(perm);
}
void treeEvaluateRandom (tree *tr, double smoothFactor, analdef *adef)
{
smoothTreeRandom(tr, (int)((double)smoothings * smoothFactor), adef);
evaluateGeneric(tr, tr->start);
}
void treeEvaluateProgressive(tree *tr)
{
int
i, k;
tr->branchCounter = 0;
tr->numberOfBranches = 2 * tr->mxtips - 3;
tr->bInf = (branchInfo*)rax_malloc(tr->numberOfBranches * sizeof(branchInfo));
setupBranches(tr, tr->start->back, tr->bInf);
assert(tr->branchCounter == tr->numberOfBranches);
for(i = 0; i < tr->numBranches; i++)
tr->partitionConverged[i] = FALSE;
for(i = 0; i < 10; i++)
{
for(k = 0; k < tr->numberOfBranches; k++)
{
update(tr, tr->bInf[k].oP);
newviewGeneric(tr, tr->bInf[k].oP);
}
evaluateGenericInitrav(tr, tr->start);
printf("It %d %f \n", i, tr->likelihood);
}
}
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