More work on the new commit infraestructure
git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1601 331e1502-861f-0410-8da2-ba01fb791d7f
This commit is contained in:
wcancino
parent
83ffb12d41
commit
121545e6d7
2 changed files with 66 additions and 32 deletions
|
|
@ -257,29 +257,32 @@ edge phylotreeIND::choose_edge_fromside_2( struct split_info *info, bool inside
|
|||
{
|
||||
edge edgeaux;
|
||||
bool chosen = false;
|
||||
int taxon_map;
|
||||
// cout << "edge recibido es internal " << info ;
|
||||
int n = number_of_taxons();
|
||||
int i=0;
|
||||
// if(info) cout << " " << info->left << " " << info->right << endl;
|
||||
do
|
||||
{
|
||||
edgeaux = select_edge();
|
||||
//cout << "edge selected is " ;
|
||||
struct split_info *info2 = interior_edge[edgeaux];
|
||||
if ( info == NULL ) return edgeaux;
|
||||
if ( info == NULL )
|
||||
return edgeaux;
|
||||
|
||||
if( is_internal(edgeaux) )
|
||||
{
|
||||
int taxon_map = splitstable[ taxon_id(edgeaux.target()) ].map_to_node;
|
||||
if( inside)
|
||||
chosen = ( taxon_map >= info->left && taxon_map <= info->right );
|
||||
else
|
||||
chosen = ( taxon_map < info->left || taxon_map > info->right );
|
||||
}
|
||||
// chosen = true edge is inside, false edge is outside
|
||||
chosen = ( info->left <= info2->left && info->right >= info2->right );
|
||||
else
|
||||
{
|
||||
if ( inside )
|
||||
chosen = ( info->left <= info2->left && info->right >= info2->right );
|
||||
else
|
||||
chosen = ( info->left > info2->right || info->right < info2->left );
|
||||
}
|
||||
|
||||
taxon_map = splitstable[ taxon_id(edgeaux.target()) ].map_to_node;
|
||||
chosen = ( taxon_map >= info->left && taxon_map <= info->right );
|
||||
|
||||
}
|
||||
i=i+1;
|
||||
}
|
||||
while( !chosen );
|
||||
while( chosen != inside );
|
||||
return edgeaux;
|
||||
}
|
||||
|
||||
|
|
@ -374,7 +377,7 @@ void phylotreeIND::init()
|
|||
|
||||
bool phylotreeIND::split2(edge edgeaux)
|
||||
{
|
||||
if (is_internal(edgeaux)) return 0;
|
||||
if (!is_internal(edgeaux)) return 0;
|
||||
struct split_info *part_info = interior_edge[edgeaux];
|
||||
return (part_info->side == 0);
|
||||
}
|
||||
|
|
@ -393,7 +396,8 @@ void phylotreeIND::crossover_gaml(phylotreeIND &TREE2)
|
|||
list<node> subtree_nodes;
|
||||
// select the root of the tree to be pruned (the root is market with 1 in the split
|
||||
// corresponding to edgeaux
|
||||
root1 = split(*edgeaux, edgeaux->source()) ? edgeaux->source() : edgeaux->target();
|
||||
//root1 = split(*edgeaux, edgeaux->source()) ? edgeaux->source() : edgeaux->target();
|
||||
root1 = split2(*edgeaux) ? edgeaux->source() : edgeaux->target();
|
||||
// select the root of the subtree pruned
|
||||
parent1 = root1 == edgeaux->source() ? edgeaux->target() : edgeaux->source();
|
||||
// save the distance of edgeaux
|
||||
|
|
@ -446,7 +450,8 @@ void phylotreeIND::export_subtree( phylotreeIND &dest)
|
|||
// save the distance of the edge comming to the root_subtree
|
||||
double dist = get_branch_length(source_edge);
|
||||
|
||||
root_subtree = split(source_edge,source_edge.source()) ? source_edge.source() : source_edge.target();
|
||||
//root_subtree = split(source_edge,source_edge.source()) ? source_edge.source() : source_edge.target();
|
||||
root_subtree = split2(source_edge) ? source_edge.source() : source_edge.target();
|
||||
// points to the parent of the subtree in order to do the percurse
|
||||
|
||||
// DEBUG INFO
|
||||
|
|
@ -510,8 +515,13 @@ void phylotreeIND::crossover_parsigal( phylotreeIND & TREE2,phylotreeIND & SON1,
|
|||
|
||||
|
||||
// works from both rooted and unrooted trees
|
||||
root1 = split(*edgeaux1,edgeaux1->source()) ? edgeaux1->source() : edgeaux1->target();
|
||||
root2 = TREE2.split(*edgeaux2,edgeaux2->source()) ? edgeaux2->source() : edgeaux2->target();
|
||||
// root1 = split(*edgeaux1,edgeaux1->source()) ? edgeaux1->source() : edgeaux1->target();
|
||||
// root2 = TREE2.split(*edgeaux2,edgeaux2->source()) ? edgeaux2->source() : edgeaux2->target();
|
||||
|
||||
root1 = split2(*edgeaux1) ? edgeaux1->source() : edgeaux1->target();
|
||||
root2 = TREE2.split2(*edgeaux2) ? edgeaux2->source() : edgeaux2->target();
|
||||
|
||||
|
||||
|
||||
// its imposible to swap the entire tree
|
||||
if(root!=NULL && (root1 == *root || root2 == *TREE2.root)) return;
|
||||
|
|
@ -893,15 +903,20 @@ void phylotreeIND::SPR()
|
|||
edge edgeaux1 = select_edge();
|
||||
//select_edge_at_pos( TREE.all_edges(), j);
|
||||
|
||||
|
||||
node nodeaux, delnode, nodeaux2;
|
||||
|
||||
// because the edgeaux will be deleted we save it split
|
||||
|
||||
int idx_begin = edgeaux1.id() * TREE.number_of_nodes();
|
||||
|
||||
struct split_info *info = is_internal(edgeaux1) ? interior_edge[edgeaux1] : NULL;
|
||||
|
||||
// save the distance of edgeaux1
|
||||
double d_edgeaux1 = get_branch_length(edgeaux1);
|
||||
|
||||
nodeaux = split(edgeaux1,edgeaux1.source()) ? edgeaux1.source() : edgeaux1.target();
|
||||
|
||||
//nodeaux = split(edgeaux1,edgeaux1.source()) ? edgeaux1.source() : edgeaux1.target();
|
||||
nodeaux = split2(edgeaux1) ? edgeaux1.source() : edgeaux1.target();
|
||||
// select the source preventing remove a taxon
|
||||
delnode = edgeaux1.opposite(nodeaux);
|
||||
// prune edge1 and graft in edge 2
|
||||
|
|
@ -911,8 +926,8 @@ void phylotreeIND::SPR()
|
|||
//TREE.del_edge(edgeaux1);
|
||||
collapse_node(delnode);
|
||||
|
||||
edge edgeaux2 = choose_edge_fromside(idx_begin, false);
|
||||
|
||||
//edge edgeaux2 = choose_edge_fromside(idx_begin, false);
|
||||
edge edgeaux2 = choose_edge_fromside_2(info, false);
|
||||
// finally, regraft in edgeaux2
|
||||
// insert the subtree rooted at nodeaux in edgeaux2;
|
||||
insert_node_in_edge(nodeaux, edgeaux2, d_edgeaux1);
|
||||
|
|
@ -932,7 +947,7 @@ void phylotreeIND::TBR()
|
|||
// the graph was divide by removing edgeaux1
|
||||
|
||||
int idx_begin = prune_edge.id() * TREE.number_of_nodes();
|
||||
|
||||
struct split_info *info = interior_edge[prune_edge];
|
||||
|
||||
source = prune_edge.source();
|
||||
dest = prune_edge.target();
|
||||
|
|
@ -942,8 +957,12 @@ void phylotreeIND::TBR()
|
|||
collapse_node(source);
|
||||
collapse_node(dest);
|
||||
|
||||
edgeaux1 = choose_edge_fromside( idx_begin, true);
|
||||
edgeaux2 = choose_edge_fromside( idx_begin, false);
|
||||
// edgeaux1 = choose_edge_fromside( idx_begin, true);
|
||||
// edgeaux2 = choose_edge_fromside( idx_begin, false);
|
||||
|
||||
edgeaux1 = choose_edge_fromside_2( info, true);
|
||||
edgeaux2 = choose_edge_fromside_2( info, false);
|
||||
|
||||
// create the new nodes to be reconected in the respective subtrees
|
||||
nodeaux1 = divide_edge(edgeaux1);
|
||||
nodeaux2 = divide_edge(edgeaux2);
|
||||
|
|
@ -967,6 +986,7 @@ void phylotreeIND::change_subtrees()
|
|||
parent_subtree1 = source_edge.opposite(root_subtree1);
|
||||
|
||||
dest_edge = select_edge_outsidetree(source_edge);
|
||||
|
||||
|
||||
bool lado = !split(dest_edge,root_subtree1);
|
||||
root_subtree2 = split(dest_edge,dest_edge.source()) == lado
|
||||
|
|
@ -1044,10 +1064,17 @@ void phylotreeIND::collapse_node(node delnode)
|
|||
adj2 = it2->opposite(delnode);
|
||||
// if adj1 is a taxon, connect adj2->adj1
|
||||
if( istaxon(adj1) )
|
||||
new_branch( adj2, adj1, get_branch_length(*it1) + get_branch_length(*it2));
|
||||
{
|
||||
edgeaux = new_branch( adj2, adj1, get_branch_length(*it1) + get_branch_length(*it2));
|
||||
//edgeaux = TREE.new_edge( adj2, adj1);
|
||||
|
||||
}
|
||||
else
|
||||
new_branch( adj1, adj2, get_branch_length(*it1) + get_branch_length(*it2));
|
||||
{
|
||||
edgeaux = new_branch( adj1, adj2, get_branch_length(*it1) + get_branch_length(*it2));
|
||||
}
|
||||
|
||||
if( !istaxon(adj1) && !istaxon(adj2) ) interior_edge[edgeaux] = interior_node[adj1];
|
||||
//edgeaux = TREE.new_edge( adj1, adj2);
|
||||
// set the new distance as the sum of edge lenghts
|
||||
//set_branch_length( edgeaux, get_branch_length(*it1) + get_branch_length(*it2) );
|
||||
|
|
@ -2212,6 +2239,7 @@ void phylotreeIND::calculate_splits4()
|
|||
int n = number_of_taxons();
|
||||
//struct split_info **hash_table; // hash that points struct info
|
||||
//struct split_info *interior_node_info = new struct split_info[n-1];
|
||||
splitstable.clear();
|
||||
splitstable.resize(n);
|
||||
|
||||
int idx_interior = 0;
|
||||
|
|
|
|||
|
|
@ -35,13 +35,19 @@ int main(int argc, char *argv[])
|
|||
phylotreeIND templatetree6( rn, seq6, rn2);
|
||||
phylotreeIND *test = templatetree6.randomClone();
|
||||
phylotreeIND test2(*test);
|
||||
test2.TBR();
|
||||
|
||||
test->calculate_splits4();
|
||||
test->print_splits_2();
|
||||
test->printNewick(cout);
|
||||
test2.calculate_splits4();
|
||||
test->export_subtree(test2);
|
||||
//test2.TBR();
|
||||
|
||||
//test2.printNewick(cout);
|
||||
cout << "calculando splits..." << endl;
|
||||
test2.calculate_splits4();
|
||||
//test->print_splits_2();
|
||||
|
||||
cout << "calculando distance..." << endl;
|
||||
cout << "distance " << test->compare_topology_4(test2) << endl;
|
||||
cout << "calculando distance..." << endl;
|
||||
cout << "distance " << test->compare_topology_2(test2) << endl;
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue