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//
// phylosupertreeunlinked.h
// tree
//
// Created by Minh Bui on 2/5/18.
//
#ifndef phylosupertreeunlinked_h
#define phylosupertreeunlinked_h
#include "phylosupertree.h"
/**
Super-tree with separate partition tree topologies
*/
class PhyloSuperTreeUnlinked : public PhyloSuperTree {
public:
/**
constructors
*/
PhyloSuperTreeUnlinked(SuperAlignment *alignment);
virtual bool isSuperTreeUnlinked() {
return true;
}
/**
read the tree from the ifstream in newick format
@param in the input stream.
@param is_rooted (IN/OUT) true if tree is rooted
*/
virtual void readTree(istream &in, bool &is_rooted);
/**
Set the alignment, important to compute parsimony or likelihood score
Assing taxa ids according to their position in the alignment
@param alignment associated alignment
*/
virtual void setAlignment(Alignment *alignment);
/**
* setup all necessary parameters (declared as virtual needed for phylosupertree)
*/
virtual void initSettings(Params& params);
/**
create sub-trees T|Y_1,...,T|Y_k of the current super-tree T
and map F={f_1,...,f_k} the edges of supertree T to edges of subtrees T|Y_i
*/
virtual void mapTrees();
/**
* FAST VERSION: compute parsimony tree by step-wise addition
* @param out_prefix prefix for .parstree file
* @param alignment input alignment
* @param rand_stream random stream
* @return parsimony score
*/
virtual int computeParsimonyTree(const char *out_prefix, Alignment *alignment, int *rand_stream);
/**
* Assign branch lengths for branch that has no or negative length
* With single model branch lengths are assigned using parsimony. With partition model
* branch lengths are assigned randomly
* @param force_change if true then force fixing also positive branch lengths
* @return number of branches fixed
*/
virtual int wrapperFixNegativeBranch(bool force_change);
/** @return true if tree is bifurcating, false otherwise */
virtual bool isBifurcating(Node *node = NULL, Node *dad = NULL);
/**
Read the tree saved with Taxon IDs and branch lengths.
@param tree_string tree string to read from
@param updatePLL if true, tree is read into PLL
*/
virtual void readTreeString(const string &tree_string);
/*
* Return the tree string contining taxon IDs and branch lengths
* @return
* @param format (WT_TAXON_ID, WT_BR_LEN, ...)
* @return the tree string with the specified format
*/
virtual string getTreeString();
/**
save object into the checkpoint
*/
virtual void saveCheckpoint();
/**
restore object from the checkpoint
*/
virtual void restoreCheckpoint();
/**
* save branch lengths into a vector
*/
virtual void saveBranchLengths(DoubleVector &lenvec, int startid = 0, PhyloNode *node = NULL, PhyloNode *dad = NULL);
/**
* restore branch lengths from a vector previously called with saveBranchLengths
*/
virtual void restoreBranchLengths(DoubleVector &lenvec, int startid = 0, PhyloNode *node = NULL, PhyloNode *dad = NULL);
/** set the root by name
@param my_root root node name
@param multi_taxa TRUE if my_root is a comma-separated list of nodes
*/
virtual void setRootNode(const char *my_root, bool multi_taxa = false);
/**
compute the weighted average of branch lengths over partitions
*/
virtual void computeBranchLengths();
/**
print the tree to the output file in newick format
@param out the output stream.
@param brtype type of branch to print
*/
virtual void printTree(ostream & out, int brtype = WT_BR_LEN);
/**
print tree to .treefile
@param params program parameters, field root is taken
*/
virtual void printResultTree(string suffix = "");
/**
@return sum of all branch lengths
@param node the starting node, NULL to start from the root
@param dad dad of the node, used to direct the search
*/
virtual double treeLength(Node *node = NULL, Node *dad = NULL);
/**
@return sum length of all internal branches
@param node the starting node, NULL to start from the root
@param dad dad of the node, used to direct the search
*/
virtual double treeLengthInternal(double epsilon, Node *node = NULL, Node *dad = NULL);
/**
* @brief Perform NNI search on the current tree topology
* @return <number_of_NNIs, number_of_NNI_steps>
* This function will automatically use the selected kernel (either PLL or IQ-TREE)
*/
virtual pair<int, int> doNNISearch(bool write_info = false);
/**
perform tree search
@return best likelihood found
*/
virtual double doTreeSearch();
/** summarize bootstrap trees */
virtual void summarizeBootstrap(Params ¶ms);
/**
write .ufboot trees file
*/
virtual void writeUFBootTrees(Params ¶ms);
/**
Test all branches of the tree with aLRT SH-like interpretation
*/
virtual int testAllBranches(int threshold, double best_score, double *pattern_lh,
int reps, int lbp_reps, bool aLRT_test, bool aBayes_test,
PhyloNode *node = NULL, PhyloNode *dad = NULL);
/**
test the best number of threads
*/
virtual int testNumThreads();
};
#endif /* phylosupertreeunlinked_h */
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