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circularnetwork.h
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circularnetwork.h
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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 CIRCULARNETWORK_H
#define CIRCULARNETWORK_H
#include "pdnetwork.h"
/**
Circular Network for PDA algorithm
@author BUI Quang Minh, Steffen Klaere, Arndt von Haeseler
*/
class CircularNetwork : public PDNetwork
{
public:
/**
empty constructor
*/
CircularNetwork();
/**
construct network from a NEXUS file, e.g. produced by SplitsTree
@param params program parameters
*/
CircularNetwork(Params ¶ms);
/**
MAIN FUNCTION which will call other other findPD depending on the input splits.
Search for maximal phylogenetic diversity of a given size
@param params program parameters
@param taxa_set (OUT) the set of taxa in the maximal PD set
@param taxa_order (OUT) order of inserted taxa
*/
virtual void findPD(Params ¶ms, vector<SplitSet> &taxa_set, vector<int> &taxa_order);
/********************************************************
Dynamic programming strategy
********************************************************/
/**
dynamic programming algorithm in UNROOTED circular splits graph
for phylogenetic diversity of a given size
@param params parameters
@param taxa_set (OUT) the set of taxa in the PD-set
@param taxa_order (IN) order of inserted taxa
*/
void findCircularPD(Params ¶ms, vector<SplitSet> &taxa_set, vector<int> &taxa_order);
/**
dynamic programming algorithm in ROOTED circular splits graph
for phylogenetic diversity of a given size
@param params parameters
@param taxa_set (OUT) the set of taxa in the PD-set
@param taxa_order (IN) order of inserted taxa
@param root index of the root taxon
*/
void findCircularRootedPD(Params ¶ms, vector<SplitSet> &taxa_set,
vector<int> &taxa_order, int root);
/**
dynamic programming algorithm with cost-constrained in UNROOTED circular splits graph
for phylogenetic diversity under budget constraint
@param params program parameters
@param taxa_set (OUT) the set of taxa in the PD-set
@param taxa_order (IN) order of inserted taxa
@return the PD score of the maximal set, also returned in taxa_set.weight
*/
void findCircularPDBudget(Params ¶ms, vector<SplitSet> &taxa_set, vector<int> &taxa_order);
/**
dynamic programming algorithm with cost-constrained in ROOTED circular splits graph
for phylogenetic diversity under budget constraint
@param params program parameters
@param taxa_set (OUT) the set of taxa in the PD-set
@param taxa_order (IN) order of inserted taxa
@return the PD score of the maximal set, also returned in taxa_set.weight
@param root index of the root taxon
*/
void findCircularRootedPDBudget(Params ¶ms, vector<SplitSet> &taxa_set,
vector<int> &taxa_order, int root);
protected:
/********************************************************
CIRCULAR NETWORKS
********************************************************/
/**
compute the PD information table
@param params program parameters
@param table (OUT) computed information
@param dist distance matrix
@param root index of the root taxon
*/
void computePDInfo(Params ¶ms, DoubleMatrix &table, DoubleMatrix &dist, int root);
/**
compute the PD score
@param sub_size the subset size
@param table computed information
@param root index of the root taxon
*/
double computePDScore(int sub_size, DoubleMatrix &table, int root);
/**
construct optimal PD set from computed information for ROOTED case circular network
@param sub_size the subset size
@param find_all TRUE of want to find all PD sets
@param pd_limit maximum number of returned PD sets
@param table computed information
@param dist distance matrix
@param taxa_set (OUT) sets of taxa with optimal PD
@param taxa_order circular order
@param root the root
*/
void constructPD(int sub_size, bool find_all, int pd_limit, DoubleMatrix &table, DoubleMatrix &dist,
SplitSet &taxa_set, vector<int> &taxa_order, int root);
/**
construct optimal PD set from computed information for ROOTED case circular network
@param sub_size the subset size
@param max_v end taxon
@param pd_limit maximum number of returned PD sets
@param pd_set the current constructed PD set
@param table computed information
@param dist distance matrix
@param taxa_set (OUT) sets of taxa with optimal PD
@param taxa_order circular order
@param root the root
*/
void constructPD(int sub_size, int max_v, int pd_limit, Split *pd_set, DoubleMatrix &table,
DoubleMatrix &dist, SplitSet &taxa_set, vector<int> &taxa_order, int root);
/********************************************************
CIRCULAR NETWORKS WITH BUDGET CONSTRAINT
********************************************************/
/**
calculate the maximum budget required from u to v (excluding u and v)
@param budget total budget
@param max_b (OUT) max budget matrix between taxa
@param taxa_order circular order
*/
void calcMaxBudget(int budget, matrix(int) &max_b, vector<int> &taxa_order);
/**
construct optimal PD set from computed information for budget constraint (ROOTED case)
@param budget total budget
@param find_all TRUE of want to find all PD sets
@param table computed information
@param dist distance matrix
@param taxa_set (OUT) sets of taxa with optimal PD
@param taxa_order circular order
@param max_b max budget matrix between taxa
@param root the root
*/
void constructPDBudget(int budget, bool find_all, matrix(double) &table,
matrix(double) &dist,SplitSet &taxa_set,
vector<int> &taxa_order, matrix(int) &max_b, int root);
/**
construct optimal PD set from computed information for budget constraint (ROOTED case)
@param budget total budget
@param max_v end taxon
@param pd_set the current constructed PD set
@param table computed information
@param dist distance matrix
@param taxa_set (OUT) sets of taxa with optimal PD
@param taxa_order circular order
@param max_b max budget matrix between taxa
@param root the root
*/
void constructPDBudget(int budget, int max_v, Split *pd_set,
matrix(double) &table, matrix(double) &dist, SplitSet &taxa_set,
vector<int> &taxa_order, matrix(int) &max_b, int root);
/**
compute the PD information table with budget
@param params program parameters
@param table (OUT) computed information
@param id (OUT) computed information
@param dist distance matrix
@param taxa_order circular order
@param max_b max budget matrix between taxa
@param root index of the root taxon
*/
void computePDBudgetInfo(Params ¶ms, matrix(double) &table, matrix(int) &id,
matrix(double) &dist, vector<int> &taxa_order, matrix(int) &max_b, int root);
/**
compute the PD score with budget
@param budget total budget
@param table (OUT) computed information
@param dist distance matrix
@param taxa_order circular order
@param max_b max budget matrix between taxa
@param root index of the root taxon
*/
double computePDBudgetScore(int budget, matrix(double) &table,
matrix(double) &dist, vector<int> &taxa_order, matrix(int) &max_b, int root);
};
/**
display the matrix into out
*/
template <class T>
ostream &operator<<(ostream &out, matrix(T) &mat) {
unsigned int i, j;
for (i = 0; i < mat.size(); i++) {
for (j = 0; j < mat[i].size(); j++) {
if (j < i)
out << " & ";
else if (j < mat[i].size()-1)
out << mat[i][j] << " & ";
else
out << mat[i][j];
}
if (i < mat.size()-1)
out << " \\\\";
out << endl;
}
return out;
}
#endif