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/***************************************************************************
* Copyright (C) 2009-2015 by *
* BUI Quang Minh <minh.bui@univie.ac.at> *
* Lam-Tung Nguyen <nltung@gmail.com> *
* *
* *
* 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 PHYLOANALYSIS_H
#define PHYLOANALYSIS_H
#include "tools.h"
#include "mexttree.h"
#include "phylotesting.h"
#include "upperbounds.h" // Olga: functions for Upper Bounds analysis
#include "pllnni.h"
class PhyloTree;
class IQTree;
/**
main function to carry out phylogenetic inference
@param params program parameters
*/
void runPhyloAnalysis(Params ¶ms, Checkpoint *checkpoint);
void runTreeReconstruction(Params ¶ms, string &original_model,
IQTree &tree, vector<ModelInfo> &model_info);
/**
take the collection of trees from input_trees, it assign support values to target_tree
and print resulting tree to output_tree.
@param input_trees collection of input trees to infer split supports
@param burnin the number trees at the beginning of input_trees to be discarded
@param max_count max number of trees to load
@param target_tree tree to assign support value
@param output_tree (OUT, OVERWRITE IF EXIST) Resulting will be written to this file. If NULL,
output_tree will be named target_tree appended with ".suptree"
*/
void assignBootstrapSupport(const char *input_trees, int burnin, int max_count, const char *target_tree,
bool rooted, const char *output_tree, const char *out_prefix, MExtTree &mytree,
const char* tree_weight_file, Params *params);
/**
* assign branch supports from params.user_tree trees file to params.second_tree
* @param params program parameters
*/
void assignBranchSupportNew(Params ¶ms);
/**
Compute the consensus tree from the collection of trees from input_trees
and print resulting tree to output_tree.
@param phylo_tree used to optimize branch lengths of the consensus tree. Can be NULL
@param input_trees collection of input trees to infer split supports
@param burnin the number trees at the beginning of input_trees to be discarded
@param max_count max number of trees to load
@param cutoff only incorporate those splits that have support values more than cutoff
@param weight_threshold minimum weight cutoff
@param output_tree (OUT, OVERWRITE IF EXIST) Resulting consensus tree will be written to this file. If NULL,
output_tree will be named input_trees appended with ".contree"
*/
void computeConsensusTree(const char *input_trees, int burnin, int max_count, double cutoff, double weight_threshold,
const char *output_tree, const char *out_prefix, const char* tree_weight_file, Params *params);
/**
Compute the consensus network from the collection of trees in input_trees.
print consensus network to output_tree
@param input_trees collection of input trees to infer split supports
@param burnin the number trees at the beginning of input_trees to be discarded
@param max_count max number of trees to load
@param cutoff only incorporate those splits that have support values more than cutoff
@param weight_threshold minimum weight cutoff
@param output_tree (OUT, OVERWRITE IF EXIST) Resulting consensus tree will be written to this file. If NULL,
output_tree will be named input_trees appended with ".connetwork"
*/
void computeConsensusNetwork(const char *input_trees, int burnin, int max_count, double cutoff,
int weight_summary, double weight_threshold,
const char *output_tree, const char *out_prefix, const char* tree_weight_file);
#endif
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