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/***************************************************************************
* Copyright (C) 2009 by BUI Quang Minh *
* minh.bui@univie.ac.at *
* *
* 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 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. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the *
* Free Software Foundation, Inc., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#ifndef GUIDED_BOOTSTRAP_H
#define GUIDED_BOOTSTRAP_H
#include "tools.h"
#include "iqtree.h"
#include "alignment.h"
struct hashfunc_IntVector {
size_t operator()(const IntVector* sp) const {
size_t sum = 0;
for (IntVector::const_iterator it = sp->begin(); it != sp->end(); it++)
sum = (*it) + (sum << 6) + (sum << 16) - sum;
return sum;
}
};
namespace std {
/**
Define equal_to of two IntVector, used for hash_set (or hash_map) template
*/
template<>
struct equal_to<IntVector*> {
/**
@return true if *s1 == *s2
@param s1 first IntVector
@param s2 second IntVector
*/
bool operator()(const IntVector* s1, const IntVector* s2) const{
return *s1 == *s2;
}
};
/**
Define less than relationship of two IntVector, used for set (or map) template
*/
template<>
struct less<IntVector*> {
/**
@return true if *s1 < *s2 alphabetically
@param s1 first IntVector
@param s2 second IntVector
*/
bool operator()(const IntVector *s1, const IntVector *s2) const {
assert(s1->size() == s2->size());
for (int i = 0; i < s1->size(); i++)
if ((*s1)[i] < (*s2)[i])
return true;
else if ((*s1)[i] > (*s2)[i]) return false;
return false;
}
};
} // namespace std
#ifdef USE_HASH_MAP
typedef unordered_map<IntVector*, int, hashfunc_IntVector> IntVectorMap;
#else
typedef map<IntVector*, int> IntVectorMap;
#endif
typedef vector<IntVector*> IntVectorCollection;
/**
OBSOLETE: run guided bootstrap (this function was only used at the beginning of the UFBoot project
*/
void runGuidedBootstrap(Params ¶ms, Alignment *alignment, IQTree &tree);
void runAvHTest(Params ¶ms, Alignment *alignment, IQTree &tree);
/**
* make the plot with x-axis being the alignments and y-axis being the likelihood of all trees
* Right now we use Kullback-Leibler distance to arrange alignments on the x-axis
*/
void runBootLhTest(Params ¶ms, Alignment *alignment, IQTree &tree);
#endif
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