nojhan/paradiseo
Watch
1
0
Fork
You've already forked paradiseo
 0
Code Issues Pull requests Projects Releases Packages Wiki Activity

New split calculation

Browse source 
git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1592 331e1502-861f-0410-8da2-ba01fb791d7f
This commit is contained in:
wcancino 2009-06-25 15:32:07 +00:00
commit 5312c3321e
6 changed files with 322 additions and 15 deletions
Download patch file Download diff file Expand all files Collapse all files

46
contribution/branches/PhyloMOEA/PhyloMOEA/phylotreeIND.h
View file

@ -36,6 +36,19 @@
#include <treeIterator.h>
#include <stack>
#include <tree_limits.h>
#include <functors.h>
struct split_info
{
int left, right, num_nodes, map_to_node, node_to_map;
split_info *hash;
split_info() {};
split_info(int n) : left(n), right(-1), num_nodes(0), hash(NULL), map_to_node(-1), node_to_map(-1) {};
bool invalid() { return right == -1; };
};
class phylotreeIND
@ -47,6 +60,11 @@ class phylotreeIND
vector<node> MAPTAXONNODE; // each taxon number points to a node
vector<edge> MAPIDEDGE;
valarray<double> NJDISTANCES; // distances stored in the edges
vector<struct split_info> splitstable;
node_map<struct split_info*> interior_node;
edge_map<struct split_info*> interior_edge;
//edge_map< node_map<int> > SPLITS; // the splits that each edge separate the graph
bool *split_bits;
Sequences *seqpatterns;
@ -59,9 +77,6 @@ class phylotreeIND
void init();
void SPR(); //SPR operator
void NNI(); // NNI operator
void TBR(); // TBR operator
void taxa_swap(); // taxa swap operator
void collapse_node ( node );
@ -75,6 +90,7 @@ class phylotreeIND
void calculate_splits_from_edge2 ( edge, node );
int split_set_edge ( edge , edge );
void print_split ( edge ) const;
void obtain_subtree ( node , node *, list <edge> *, list<node> * );
void construct_graph ( const phylotreeIND &, list <node>& , list <edge>& );
void change_subtrees();
@ -113,6 +129,9 @@ class phylotreeIND
virtual phylotreeIND* clone() const;
virtual phylotreeIND* randomClone() const;
void SPR(); //SPR operator
void NNI(); // NNI operator
void TBR(); // TBR operator
GTL::graph TREE; // final tree calculated by NJ
// constructors
@ -135,6 +154,7 @@ class phylotreeIND
void convert_graph_to_tree ( node, node * );
void calculate_splits();
void calculate_splits4();
void calculate_splits_exp();
inline void invalidate_splits() { valid_splits = false; }
inline void remove_split_memory()
@ -150,6 +170,7 @@ class phylotreeIND
}
string get_split_key ( edge edgeaux ) const;
string get_split_key_2 ( edge edgeaux ) const;
string get_invert_split_key ( edge edgeaux ) const;
bool is_internal ( edge ) const;
@ -192,9 +213,10 @@ class phylotreeIND
double compare_topology ( phylotreeIND &other );
double compare_topology_2 ( phylotreeIND &other );
double compare_topology_3 ( phylotreeIND &other );
double compare_topology_4(phylotreeIND &other);
double robinson_foulds_distance ( phylotreeIND &other, int debug=0 );
void print_splits_2 ( ) const;
// iterator
postorder_Iterator postorder_begin ( node root, node father ) const
{
@ -286,5 +308,21 @@ class phylotreeIND
};
template<typename T> const T& select_edge_at_pos ( const list <T> &, int );
template <class R>
class TreeCalculator : public FunctorUnary<phylotreeIND &, R>
{
public :
/// virtual dtor here so there is no need to define it in derived classes
virtual ~TreeCalculator() {}
/// The pure virtual function that needs to be implemented by the subclass
virtual R operator()(phylotreeIND &) = 0;
};
#endif