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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 PHYLOSUPERTREE_H
#define PHYLOSUPERTREE_H
#include "iqtree.h"
#include "supernode.h"
#include "superalignment.h"
/**
Phylogenetic tree for partition model (multi-gene alignment)
@author BUI Quang Minh <minh.bui@univie.ac.at>
*/
class PhyloSuperTree : public IQTree, public vector<PhyloTree* >
{
public:
/**
constructor
*/
PhyloSuperTree();
/**
constructor
*/
PhyloSuperTree(SuperAlignment *alignment, PhyloSuperTree *super_tree);
/**
constructor
*/
PhyloSuperTree(Params ¶ms);
~PhyloSuperTree();
/**
set checkpoint object
@param checkpoint
*/
virtual void setCheckpoint(Checkpoint *checkpoint);
/**
save object into the checkpoint
*/
virtual void saveCheckpoint();
/**
restore object from the checkpoint
*/
virtual void restoreCheckpoint();
/** read partition model file */
void readPartition(Params ¶ms);
/** read RAxML-style partition file */
void readPartitionRaxml(Params ¶ms);
/** read partition model file in NEXUS format into variable info */
void readPartitionNexus(Params ¶ms);
void printPartition(const char *filename);
void printPartitionRaxml(const char *filename);
void printBestPartition(const char *filename);
void printBestPartitionRaxml(const char *filename);
/** remove identical sequences from the tree */
virtual void removeIdenticalSeqs(Params ¶ms);
/** reinsert identical sequences into the tree and reset original alignment */
virtual void reinsertIdenticalSeqs(Alignment *orig_aln);
virtual void setParams(Params* params);
/**
* setup all necessary parameters (declared as virtual needed for phylosupertree)
*/
virtual void initSettings(Params& params);
virtual void setLikelihoodKernel(LikelihoodKernel lk, int num_threads);
virtual void changeLikelihoodKernel(LikelihoodKernel lk);
virtual bool isSuperTree() { return true; }
/**
* Return the tree string contining taxon names and branch lengths
* @return
*/
virtual string getTreeString();
/**
Read the tree saved with Taxon Names 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);
/**
* 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);
/**
allocate a new node. Override this if you have an inherited Node class.
@param node_id node ID
@param node_name node name
@return a new node
*/
virtual Node* newNode(int node_id = -1, const char* node_name = NULL);
/**
allocate a new node. Override this if you have an inherited Node class.
@param node_id node ID
@param node_name node name issued by an interger
@return a new node
*/
virtual Node* newNode(int node_id, int node_name);
/**
* @return number of alignment patterns
*/
virtual int getAlnNPattern();
/**
* @return number of alignment sites
*/
virtual int getAlnNSite();
/**
compute the distance between 2 sequences.
@param seq1 index of sequence 1
@param seq2 index of sequence 2
@param initial_dist initial distance
@return distance between seq1 and seq2
*/
virtual double computeDist(int seq1, int seq2, double initial_dist, double &var);
/**
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();
/*
* create one map f_i from supertree T to subtree indexed by part (called by mapTrees)
* @param part index of subtree
* @param part_taxa vector of taxa of T that are present in subtree
* @param node the current node of the post-order tree traversal
* @param dad the dad of that node used to direct the traversal
*/
void linkTree(int part, NodeVector &part_taxa, SuperNode *node = NULL, SuperNode *dad = NULL);
/**
* Given current supertree T and subtrees T|Y_1,...,T|Y_k, build all maps f_1,...,f_k
*/
virtual void linkTrees();
/**
* link a branch from supertree to subtree (called by linkTree)
* @param part index of subtree
* @param nei pointer to branch
* @param dad_nei pointer to reverse branch
*/
void linkBranch(int part, SuperNeighbor *nei, SuperNeighbor *dad_nei);
/**
initialize partial_lh vector of all PhyloNeighbors, allocating central_partial_lh
*/
virtual void initializeAllPartialLh();
/**
de-allocate central_partial_lh
*/
virtual void deleteAllPartialLh();
/**
NEWLY ADDED (2014-12-04): clear all partial likelihood for a clean computation again
*/
virtual void clearAllPartialLH(bool make_null = false);
/**
compute the tree likelihood
@param pattern_lh (OUT) if not NULL, the function will assign pattern log-likelihoods to this vector
assuming pattern_lh has the size of the number of patterns
@return tree likelihood
*/
virtual double computeLikelihood(double *pattern_lh = NULL);
/**
* @return number of elements per site lhl entry, used in conjunction with computePatternLhCat
*/
virtual int getNumLhCat(SiteLoglType wsl);
/**
compute pattern likelihoods only if the accumulated scaling factor is non-zero.
Otherwise, copy the pattern_lh attribute
@param pattern_lh (OUT) pattern log-likelihoods,
assuming pattern_lh has the size of the number of patterns
@param cur_logl current log-likelihood (for sanity check)
@param pattern_lh_cat (OUT) if not NULL, store all pattern-likelihood per category
*/
virtual void computePatternLikelihood(double *pattern_lh, double *cur_logl = NULL,
double *pattern_lh_cat = NULL, SiteLoglType wsl = WSL_RATECAT);
/**
compute pattern posterior probabilities per rate/mixture category
@param pattern_prob_cat (OUT) all pattern-probabilities per category
@param wsl either WSL_RATECAT, WSL_MIXTURE or WSL_MIXTURE_RATECAT
*/
virtual void computePatternProbabilityCategory(double *pattern_prob_cat, SiteLoglType wsl);
/**
optimize all branch lengths of all subtrees, then compute branch lengths
of supertree as weighted average over all subtrees
@param iterations number of iterations to loop through all branches
@return the likelihood of the tree
*/
virtual double optimizeAllBranches(int my_iterations = 100, double tolerance = TOL_LIKELIHOOD, int maxNRStep = 100);
/**
search the best swap for a branch
@return NNIMove The best Move/Swap
@param cur_score the current score of the tree before the swaps
@param node1 1 of the 2 nodes on the branch
@param node2 1 of the 2 nodes on the branch
*/
virtual NNIMove getBestNNIForBran(PhyloNode *node1, PhyloNode *node2, NNIMove *nniMoves = NULL);
/**
Do an NNI on the supertree and synchronize all subtrees respectively
@param move the single NNI
*/
virtual void doNNI(NNIMove &move, bool clearLH = true);
/**
* Apply 5 new branch lengths stored in the NNI move
* @param nnimove the NNI move currently in consideration
*/
virtual void changeNNIBrans(NNIMove nnimove);
/**
OBSOLETE!
* Restore the branch lengths from the saved values
* @param node the current node of the post-order tree traversal
* @param dad the dad of that node used to direct the traversal
*/
// virtual void restoreAllBrans(PhyloNode *node = NULL, PhyloNode *dad = NULL);
/**
reinsert the whole list of leaves back into the supertree then call mapTrees
@param del_leaves the list of deleted leaves, returned by deleteLeaves() function
*/
virtual void reinsertLeaves(PhyloNodeVector &del_leaves);
/**
compute the weighted average of branch lengths over partitions
*/
virtual void computeBranchLengths();
/**
* print debug information about all maps
*/
virtual void printMapInfo();
/**
* initialize partition information for super tree
*/
virtual void initPartitionInfo();
int getMaxPartNameLength();
/**
partition information
*/
vector<PartitionInfo> part_info;
/* partition ID sorted in descending order of computation cost */
IntVector part_order;
IntVector part_order_by_nptn;
/* compute part_order vector */
void computePartitionOrder();
/**
get the name of the model
*/
virtual string getModelName();
/**
* extract subtree containing all taxa from partition IDs
* @param ids partitions IDs
* @return subtree
*/
PhyloTree *extractSubtree(IntVector &ids);
/**
* compute the memory size required for storing partial likelihood vectors
* @return memory size required in bytes
*/
virtual uint64_t getMemoryRequired(size_t ncategory = 1, bool full_mem = false);
/**
* count the number of super branches that map to no branches in gene trees
*/
int countEmptyBranches(PhyloNode *node = NULL, PhyloNode *dad = NULL);
/**
Neighbor-joining/parsimony tree might contain negative branch length. This
function will fix this.
@param fixed_length fixed branch length to set to negative branch lengths
@param node the current node
@param dad dad of the node, used to direct the search
@return The number of branches that have no/negative length
*/
virtual int fixNegativeBranch(bool force = false, Node *node = NULL, Node *dad = NULL);
virtual int computeParsimonyBranchObsolete(PhyloNeighbor *dad_branch, PhyloNode *dad, int *branch_subst = NULL);
/** True when mixed codon with other data type */
bool rescale_codon_brlen;
int totalNNIs, evalNNIs;
};
#endif
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