First commit of PhyloMOEO files with some additions to Paradiseo-MOEO
git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1335 331e1502-861f-0410-8da2-ba01fb791d7f
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contribution/branches/PhyloMOEA/PhyloMOEA/phylotreeIND.h
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contribution/branches/PhyloMOEA/PhyloMOEA/phylotreeIND.h
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/***************************************************************************
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* Copyright (C) 2005 by Waldo Cancino *
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* wcancino@icmc.usp.br *
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* *
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* This program is free software; you can redistribute it and/or modify *
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* it under the terms of the GNU General Public License as published by *
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* the Free Software Foundation; either version 2 of the License, or *
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* (at your option) any later version. *
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* *
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* This program is distributed in the hope that it will be useful, *
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* but WITHOUT ANY WARRANTY; without even the implied warranty of *
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
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* GNU General Public License for more details. *
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* *
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* You should have received a copy of the GNU General Public License *
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* along with this program; if not, write to the *
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* Free Software Foundation, Inc., *
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* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
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***************************************************************************/
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#ifdef HAVE_CONFIG_H
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#include <config.h>
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#endif
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#ifndef _phylotreeIND_H_
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#define _phylotreeIND_H_
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#define BL_MIN 1.e-10
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#include <RandomNr.h>
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#include <GTL/graph.h>
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#include <gsl/gsl_rng.h>
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#include <valarray>
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#include <Sequences.h>
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#include <treeIterator.h>
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#include <stack>
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#include <tree_limits.h>
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class phylotreeIND
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{
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private:
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bool valid_splits;
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edge invalid_edge;
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node_map<int> MAPNODETAXON; // ecah node maps a taxon id in the vector
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vector<node> MAPTAXONNODE; // each taxon number points to a node
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vector<edge> MAPIDEDGE;
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valarray<double> NJDISTANCES; // distances stored in the edges
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//edge_map< node_map<int> > SPLITS; // the splits that each edge separate the graph
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bool *split_bits;
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Sequences *seqpatterns;
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int nnode; // number of nodes
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static double randomgsl_alpha; // shape paramter of gamma distribution
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gsl_rng *random_gsl; // GSL (GNU Scientific Library) random generator for gamma numbers)
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node *root;
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int parsimony;
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void init();
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void SPR(); //SPR operator
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void NNI(); // NNI operator
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void TBR(); // TBR operator
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void taxa_swap(); // taxa swap operator
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void collapse_node ( node );
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void insert_root ( edge );
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node divide_edge ( edge );
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void insert_node_in_edge ( node, edge, double d=0 );
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bool isparent ( node, node ) const;
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node firstcommonancestor ( node, node ) const;
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node firstcommonancestor ( list<node> & ) const;
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void calculate_splits_from_edge2 ( edge, node );
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int split_set_edge ( edge , edge );
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void print_split ( edge ) const;
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void obtain_subtree ( node , node *, list <edge> *, list<node> * );
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void construct_graph ( const phylotreeIND &, list <node>& , list <edge>& );
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void change_subtrees();
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void separate_subtree_from_edge ( edge, list<edge> &, bool );
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void crossover_gaml ( phylotreeIND & );
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void crossover_parsigal ( phylotreeIND &,phylotreeIND &, phylotreeIND & );
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void crossover_gaphyl ( phylotreeIND & );
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void invert_split ( edge );
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void remove_taxon ( int );
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void start_decomposition();
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void stepwise_addition();
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void separategraphs ( edge , list<edge> &, list<edge> & );
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void visit_edges_from_node ( node, list<edge> & );
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void mutate_branch_lenght ( float );
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edge select_edge_outsidetree ( edge source_edge ) const;
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edge choose_edge_fromside ( int id, bool side ) const;
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edge choose_neighboor ( edge, node ) const;
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int read_taxonname_bl ( string &s, string &taxonname, double &blen, int &pos );
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int read_bl ( string &s, double &blen, int &pos );
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edge new_branch ( node, node );
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edge new_branch ( node, node, double );
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void remove_branch ( edge );
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void reconnect_nodes ( node source, node dest );
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node new_taxon ( int id );
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node new_internal_node();
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public:
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RandomNr *randomNr;
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phylotreeIND& operator= (const phylotreeIND& ind) { copy(ind); return *this; }
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virtual phylotreeIND* clone() const;
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virtual phylotreeIND* randomClone() const;
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GTL::graph TREE; // final tree calculated by NJ
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// constructors
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void loadsequences ( char * );
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void copy ( const phylotreeIND & );
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edge select_edge() const;
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phylotreeIND ( const phylotreeIND &org );
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phylotreeIND ( RandomNr *g, Sequences &p, gsl_rng *gslr );
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~phylotreeIND();
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// genetic operators
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void export_subtree ( phylotreeIND &dest );
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virtual void crossover ( float pcross, const phylotreeIND& dad, phylotreeIND*& sis, phylotreeIND*& bro ) const;
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virtual void mutate ( float pcross );
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//IND& operator= (const IND& ind) { copy( (phylotreeIND &)ind); return *this; }
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//phylotreeIND& operator= (phylotreeIND& ind) { copy(ind); return *this; }
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edge choose_internal_edge() const;
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void convert_graph_to_tree ( node, node * );
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void calculate_splits();
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void calculate_splits_exp();
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inline void invalidate_splits() { valid_splits = false; }
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inline void remove_split_memory()
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{
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if ( split_bits!=NULL ) delete [] split_bits;
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invalidate_splits();
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split_bits=NULL;
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}
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inline void allocate_split_memory()
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{
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if ( split_bits==NULL ) split_bits = new bool [ ( 2*nnode-3 ) * ( 2*nnode-2 ) ];
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}
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string get_split_key ( edge edgeaux ) const;
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string get_invert_split_key ( edge edgeaux ) const;
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bool is_internal ( edge ) const;
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void print_splits() const;
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void set_data ( Sequences &s );
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void collapse_zero_edges();
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inline double get_branch_length ( edge edgeaux ) const { return NJDISTANCES[edgeaux.id() ]; }
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inline int taxon_id ( node nodeaux ) const { return MAPNODETAXON[nodeaux]; }
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inline int number_of_taxons() const { return seqpatterns->num_seqs(); }
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inline const Sequences & get_patterns() { return *seqpatterns; }
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inline Sequences *get_patterns2() { return seqpatterns; }
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inline node taxon_number ( int n ) const { return MAPTAXONNODE[n]; };
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inline int number_of_positions() const { return seqpatterns->pattern_count(); }
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inline void set_branch_length ( edge edgeaux, double f )
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{
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if ( f < BL_MIN )
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NJDISTANCES[edgeaux.id() ] = BL_MIN;
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else if ( f> BL_MAX )
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NJDISTANCES[edgeaux.id() ] = BL_MAX;
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else
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NJDISTANCES[edgeaux.id() ] = f;
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}
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inline bool istaxon ( node nodeaux ) const { return ( nodeaux.degree() <= 1 ); }
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inline edge edge_number ( int n ) const { return MAPIDEDGE[n]; }
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inline bool splits_valid() const { return valid_splits; }
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inline bool split ( edge edgeaux, node nodeaux ) const
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{ return split_bits[ edgeaux.id() * TREE.number_of_nodes() + nodeaux.id() ]; }
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void read_newick ( string newickstring );
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void read_newick2 ( string newickstring );
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void printtree() const;
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void printtreeinfo() const;
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void printNewick ( ostream &os );
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void newick_traverse ( node n, node *ancestor, edge edgeaux, string &s );
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string newick_traverse2 ( bool brlens=true, bool longnames=true );
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double compare_topology ( phylotreeIND &other );
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double compare_topology_2 ( phylotreeIND &other );
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double compare_topology_3 ( phylotreeIND &other );
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double robinson_foulds_distance ( phylotreeIND &other, int debug=0 );
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// iterator
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postorder_Iterator postorder_begin ( node root, node father ) const
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{
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postorder_Iterator it = postorder_Iterator ( root, father );
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it.first_node();
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return it;
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}
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postorder_Iterator postorder_begin ( node root ) const
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{
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postorder_Iterator it = postorder_Iterator ( root );
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it.first_node();
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return it;
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}
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preorder_Iterator preorder_begin ( node root, node father ) const
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{
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preorder_Iterator it = preorder_Iterator ( root, father );
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it.first_node();
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return it;
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}
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preorder_Iterator preorder_begin ( node root ) const
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{
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preorder_Iterator it = preorder_Iterator ( root );
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it.first_node();
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return it;
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}
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postorder_Iterator postorder_end ( node root, node father ) const
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{
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postorder_Iterator it = postorder_Iterator ( root, father );
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it.last_node();
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return it;
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}
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postorder_Iterator postorder_end ( node root ) const
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{
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postorder_Iterator it = postorder_Iterator ( root );
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it.last_node();
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return it;
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}
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preorder_Iterator preorder_end ( node root, node father ) const
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{
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preorder_Iterator it = preorder_Iterator ( root, father );
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it.last_node();
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return it;
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}
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preorder_Iterator preorder_end ( node root ) const
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{
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preorder_Iterator it = preorder_Iterator ( root );
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it.last_node();
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return it;
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}
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child_Iterator child_begin ( node root, node father ) const
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{
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child_Iterator it = child_Iterator ( root, father );
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it.first_node();
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return it;
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}
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child_Iterator child_begin ( node root ) const
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{
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child_Iterator it = child_Iterator ( root );
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it.first_node();
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return it;
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}
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child_Iterator child_end ( node root, node father ) const
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{
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child_Iterator it = child_Iterator ( root, father );
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it.last_node();
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return it;
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}
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child_Iterator child_end ( node root ) const
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{
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child_Iterator it = child_Iterator ( root );
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it.last_node();
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return it;
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}
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};
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template<typename T> const T& select_edge_at_pos ( const list <T> &, int );
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#endif
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