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/***************************************************************************
* Copyright (C) 2006 by BUI Quang Minh, Steffen Klaere, Arndt von Haeseler *
* 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 MEXTTREE_H
#define MEXTTREE_H
#include "mtree.h"
#include "mtreeset.h"
/**
extended tree, for bootstrap, cluster, etc (do not related to PDA main topic)
@author BUI Quang Minh, Steffen Klaere, Arndt von Haeseler
*/
class MExtTree : public MTree
{
public:
/********************************************************
CONSTRUCTORs, INITIALIZATION AND DESTRUCTORs
********************************************************/
/**
constructor, read tree from user file
@param userTreeFile the name of the user tree
@param is_rooted (IN/OUT) true if tree is rooted
*/
MExtTree(const char *userTreeFile, bool &is_rooted) : MTree(userTreeFile, is_rooted) {};
/**
constructor, get from another tree
@param tree another MTree
*/
MExtTree(MTree &tree) : MTree(tree) {};
/**
constructor
*/
MExtTree() : MTree() {};
/********************************************************
GENERATE RANDOM TREE PROCEDURES
********************************************************/
/**
generate a random tree with given tree type
@param tree_type can be YULE_HARDING, UNIFORM, BALANCED, or CATERPILLAR, or STAR_TREE
@param params program parameters
@param binary TRUE if you want to generate a binary tree
*/
void generateRandomTree(TreeGenType tree_type, Params ¶ms, bool binary = true);
/**
generate a random tree following Yule-Harding model
@param params program parameters
@param binary TRUE if you want to generate a binary tree
*/
void generateYuleHarding(Params ¶ms, bool binary = true);
/**
generate a random tree following Yule-Harding model satisfying a constraint tree
@param params program parameters
@param binary TRUE if you want to generate a binary tree
@param constraint_tree a (multifurcating) constraint tree
@param taxnames taxa names
*/
void generateConstrainedYuleHarding(Params ¶ms, MTree* constraint_tree, StrVector &taxnames);
/**
generate a random tree following uniform model
@param size number of taxa
@param binary TRUE if you want to generate a binary tree
*/
void generateUniform(int size, bool binary = true);
/**
generate a caterpillar tree
@param size number of taxa
*/
void generateCaterpillar(int size);
/**
generate a balanced tree
@param size number of taxa
*/
void generateBalanced(int size);
/**
generate a star tree
@param params program parameters
*/
void generateStarTree(Params ¶ms);
/**
* generate random branch lengths on the given topology
* @param params program parameters
*/
void generateRandomBranchLengths(Params ¶ms, Node* node = NULL, Node *dad = NULL);
/**
set the leaf ID and names when generating random tree
@param myleaves vector of leaves
*/
void setLeavesName(NodeVector &myleaves);
void setZeroInternalBranches(int num_zero_len);
/********************************************************
CLUSTER for each branch, useful for likelihood mapping analysis
********************************************************/
/**
create CLUSTER for each branch, useful for likelihood mapping analysis
@param taxa an order of taxa
@param clusters (OUT) list of all clusters
@param node the starting node, NULL to start from the root
@param dad dad of the node, used to direct the search
*/
void createCluster(NodeVector &taxa, mmatrix(int) &clusters, Node *node = NULL, Node *dad = NULL);
/**
create CLUSTER for each branch, useful for likelihood mapping analysis
@param clu_num cluster number
@param node the starting node, NULL to start from the root
@param dad dad of the node, used to direct the search
*/
void createCluster(int clu_num, Node *node, Node *dad);
/********************************************************
Miscellaneous
********************************************************/
/**
collapse all branches with support lower than minsup (in back-slash separated format)
implemented for Ricardo
*/
void collapseLowBranchSupport(DoubleVector &minsup, Node *node = NULL, Node *dad = NULL);
};
#endif
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