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/**
* PLL (version 1.0.0) a software library for phylogenetic inference
* Copyright (C) 2013 Tomas Flouri and Alexandros Stamatakis
*
* Derived from
* RAxML-HPC, a program for sequential and parallel estimation of phylogenetic
* trees by Alexandros Stamatakis
*
* This program is free software: you can redistribute it and/or modify it
* under the terms of the GNU General Public License as published by the Free
* Software Foundation, either version 3 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.
*
* You should have received a copy of the GNU General Public License along with
* this program. If not, see <http://www.gnu.org/licenses/>.
*
* For any other enquiries send an Email to Tomas Flouri
* Tomas.Flouri@h-its.org
*
* When publishing work that uses PLL please cite PLL
*
* @file randomTree.c
*/
#include "mem_alloc.h"
#include <math.h>
#include <time.h>
#include <stdlib.h>
#include <stdio.h>
#include <assert.h>
#include "pll.h"
#include "pllInternal.h"
static void insertTaxon (nodeptr p, nodeptr q)
{
nodeptr r;
r = q->back;
hookupDefault(p->next, q);
hookupDefault(p->next->next, r);
}
static nodeptr buildNewTip (pllInstance *tr, nodeptr p)
{
nodeptr q;
q = tr->nodep[(tr->nextnode)++];
hookupDefault(p, q);
q->next->back = (nodeptr)NULL;
q->next->next->back = (nodeptr)NULL;
return q;
}
static void buildSimpleTreeRandom (pllInstance *tr, int ip, int iq, int ir)
{
nodeptr
p,
s;
int
i;
i = PLL_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]);
s = buildNewTip(tr, tr->nodep[ir]);
insertTaxon(s, p);
}
static int randomInt(int n, pllInstance *tr)
{
int
res = (int)((double)(n) * randum(&tr->randomNumberSeed));
assert(res >= 0 && res < n);
return res;
}
void makePermutation(int *perm, int n, pllInstance *tr)
{
int
i,
j,
k;
for (i = 1; i <= n; i++)
perm[i] = i;
for (i = 1; i <= n; i++)
{
k = randomInt(n + 1 - i, tr); /*(int)((double)(n + 1 - i) * randum(&tr->randomNumberSeed));*/
assert(i + k <= n);
j = perm[i];
perm[i] = perm[i + k];
perm[i + k] = j;
}
}
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)));
}
}
void pllMakeRandomTree(pllInstance *tr)
{
nodeptr
p,
f,
randomBranch,
*branches = (nodeptr *)rax_malloc(sizeof(nodeptr) * (2 * tr->mxtips));
int
nextsp,
*perm = (int *)rax_malloc((tr->mxtips + 1) * sizeof(int)),
branchCounter;
makePermutation(perm, tr->mxtips, tr);
tr->ntips = 0;
tr->nextnode = tr->mxtips + 1;
buildSimpleTreeRandom(tr, perm[1], perm[2], perm[3]);
while(tr->ntips < tr->mxtips)
{
nextsp = ++(tr->ntips);
p = tr->nodep[perm[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, tr)];
insertTaxon(p->back, randomBranch);
}
rax_free(perm);
rax_free(branches);
}
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