void Node::check_valid_graph() const
{
vector<Site> *sites = sequence->get_sites();
for(unsigned int i=0;i<sites->size();i++)
{
Site *ssite = &sites->at(i);
if( ssite->has_fwd_edge() )
{
Edge *edge = ssite->get_first_fwd_edge();
Site *esite = &sites->at(edge->get_end_site_index());
if(!esite->contains_bwd_edge(edge,true))
{
Log_output::write_out("Node: site "+Log_output::itos(i)+" has fwd edge from "+Log_output::itos(edge->get_start_site_index())+
" to "+Log_output::itos(edge->get_end_site_index())+" but no return\n",1);
}
while( ssite->has_next_fwd_edge() )
{
edge = ssite->get_next_fwd_edge();
esite = &sites->at(edge->get_end_site_index());
if(!esite->contains_bwd_edge(edge,true))
{
Log_output::write_out("Node: site "+Log_output::itos(i)+" has fwd edge from "+Log_output::itos(edge->get_start_site_index())+
" to "+Log_output::itos(edge->get_end_site_index())+" but no return\n",1);
}
}
}
if( ssite->has_bwd_edge() )
{
Edge *edge = ssite->get_first_bwd_edge();
Site *esite = &sites->at(edge->get_start_site_index());
if(!esite->contains_fwd_edge(edge,true))
{
Log_output::write_out("Node: site "+Log_output::itos(i)+" has bwd edge from "+Log_output::itos(edge->get_start_site_index())+
" to "+Log_output::itos(edge->get_end_site_index())+" but no return\n",1);
}
while( ssite->has_next_bwd_edge() )
{
edge = ssite->get_next_bwd_edge();
esite = &sites->at(edge->get_start_site_index());
if(!esite->contains_fwd_edge(edge,true))
{
Log_output::write_out("Node: site "+Log_output::itos(i)+" has bwd edge from "+Log_output::itos(edge->get_start_site_index())+
" to "+Log_output::itos(edge->get_end_site_index())+" but no return\n",1);
}
}
}
}
}
void Node::write_metapost_alignment_graph(ostream *output, ostream *output2, int *count, int root_length) const throw (Exception)
{
vector<Site> *sites = this->sequence->get_sites();
vector<int> left_child_index;
vector<int> right_child_index;
for(unsigned int i=0;i<sites->size();i++)
{
Site_children *offspring = sites->at(i).get_children();
if(offspring->left_index>=0)
{
left_child_index.push_back(i);
}
if(offspring->right_index>=0)
{
right_child_index.push_back(i);
}
}
*output<<"beginfig("<<*count<<");\npickup pencircle scaled 1pt;\npath l[]; path r[];\ndefaultscale := 0.5;\n";
string full_alphabet = this->sequence->get_full_alphabet();
*output<<"l0 = circle((0cm,1.5cm),\"s\",white);\n";
*output<<"r0 = circle((0cm,0cm),\"s\",white);\n";
stringstream all_chars;
for(unsigned int i=1;i<sites->size();i++)
{
Site_children *offspring = sites->at(i).get_children();
if(offspring->left_index>=0)
{
Site *lsite = this->left_child->get_sequence()->get_site_at(offspring->left_index);
char lc = 's';
if(lsite->get_site_type()==Site::real_site || lsite->get_site_type()==Site::non_real)
lc = full_alphabet.at(lsite->get_state());
else if(lsite->get_site_type()==Site::stop_site)
lc = 'e';
string color = this->get_node_fill_color(lc);
if(lsite->get_branch_count_since_last_used()>0)
color = "0.5white";
*output<<"l"<<i<<" = circle"<<"(("<<0.5*i<<"cm,1.5cm),\""<<lc<<"\","<<color<<");\n";
}
if(offspring->right_index>=0)
{
Site *rsite = this->right_child->get_sequence()->get_site_at(offspring->right_index);
char rc = 's';
if(rsite->get_site_type()==Site::real_site || rsite->get_site_type()==Site::non_real)
rc = full_alphabet.at(rsite->get_state());
else if(rsite->get_site_type()==Site::stop_site)
rc = 'e';
string color = this->get_node_fill_color(rc);
if(rsite->get_branch_count_since_last_used()>0)
color = "0.5white";
*output<<"r"<<i<<" = circle"<<"(("<<0.5*i<<"cm,0cm),\""<<rc<<"\","<<color<<");\n";
}
}
if(left_child->is_leaf())
*output<<"label.top(btex $"<<left_child->get_name()<<"$ etex,(0.125cm,1.75cm));\n";
else
{
string n = left_child->get_name();
n = n.substr(1,n.length()-2);
*output<<"label.top(btex \\#"<<n<<"\\# etex,(0.125cm,1.75cm));\n";
}
if(right_child->is_leaf())
*output<<"label.top(btex $"<<right_child->get_name()<<"$ etex,(0.125cm,0.25cm));\n";
else
{
string n = right_child->get_name();
n = n.substr(1,n.length()-2);
*output<<"label.top(btex \\#"<<n<<"\\# etex,(0.125cm,0.25cm));\n";
}
*output<<"defaultscale := 0.25;\n";
for(unsigned int i=1;i<sites->size();i++)
{
Site_children *offspring = sites->at(i).get_children();
if(offspring->left_index>=0)
{
Site *tsite = left_child->get_sequence()->get_site_at(offspring->left_index);
if(tsite->has_bwd_edge())
{
Edge *tedge = tsite->get_first_bwd_edge();
int start = tedge->get_start_site_index();
int stop = tedge->get_end_site_index();
int angle = 0;
string place = "edgetop";
if(start+1==stop)
place = "edgebot";
else if(start+2==stop)
angle = 40;
else if(start+3==stop)
angle = 30;
else if(start+4<=stop)
angle = 20;
start = left_child_index.at( start );
stop = left_child_index.at( stop );
stringstream label;
if(tedge->get_branch_count_since_last_used()>0)
label<<"["<<tedge->get_branch_count_since_last_used()<<" "<<tedge->get_branch_count_as_skipped_edge()<<" "<<tedge->get_branch_distance_since_last_used()<<"]";
*output<<place<<"(l"<<start<<",l"<<stop<<","<<angle<<",\""<<label.str()<<"\",0.5);\n";
while(tsite->has_next_bwd_edge())
{
tedge = tsite->get_next_bwd_edge();
start = tedge->get_start_site_index();
stop = tedge->get_end_site_index();
angle = 0;
place = "edgetop";
if(start+1==stop)
place = "edgebot";
else if(start+2==stop)
angle = 40;
else if(start+3==stop)
angle = 30;
else if(start+4<=stop)
angle = 20;
start = left_child_index.at( start );
stop = left_child_index.at( stop );
label.str("");
if(tedge->get_branch_count_since_last_used()>0)
label<<"["<<tedge->get_branch_count_since_last_used()<<"~"<<tedge->get_branch_count_as_skipped_edge()<<"~"<<tedge->get_branch_distance_since_last_used()<<"]";
*output<<place<<"(l"<<start<<",l"<<stop<<","<<angle<<",\""<<label.str()<<"\",0.5);\n";
}
}
}
if(offspring->right_index>=0)
{
Site *tsite = right_child->get_sequence()->get_site_at(offspring->right_index);
if(tsite->has_bwd_edge())
{
Edge *tedge = tsite->get_first_bwd_edge();
int start = tedge->get_start_site_index();
int stop = tedge->get_end_site_index();
// int angle = 0;
// string place = "edgebot";
// if(start+1==stop)
// place = "edgetop";
// else if(start+2==stop)
// angle = 320;
// else if(start+3==stop)
// angle = 330;
// else if(start+4<=stop)
// angle = 340;
int angle = 0;
string place = "edgetop";
if(start+1==stop)
place = "edgebot";
else if(start+2==stop)
angle = 40;
else if(start+3==stop)
angle = 30;
else if(start+4<=stop)
angle = 20;
start = right_child_index.at( start );
stop = right_child_index.at( stop );
stringstream label;
if(tedge->get_branch_count_since_last_used()>0)
label<<"["<<tedge->get_branch_count_since_last_used()<<"~"<<tedge->get_branch_count_as_skipped_edge()<<"~"<<tedge->get_branch_distance_since_last_used()<<"]";
*output<<place<<"(r"<<start<<",r"<<stop<<","<<angle<<",\""<<label.str()<<"\",0.5);\n";
while(tsite->has_next_bwd_edge())
{
tedge = tsite->get_next_bwd_edge();
start = tedge->get_start_site_index();
stop = tedge->get_end_site_index();
// angle = 0;
// place = "edgebot";
// if(start+1==stop)
// place = "edgetop";
// else if(start+2==stop)
// angle = 320;
// else if(start+3==stop)
// angle = 330;
// else if(start+4<=stop)
// angle = 340;
angle = 0;
place = "edgetop";
if(start+1==stop)
place = "edgebot";
else if(start+2==stop)
angle = 40;
else if(start+3==stop)
angle = 30;
else if(start+4<=stop)
angle = 20;
start = right_child_index.at( start );
stop = right_child_index.at( stop );
label.str("");
if(tedge->get_branch_count_since_last_used()>0)
label<<"["<<tedge->get_branch_count_since_last_used()<<"~"<<tedge->get_branch_count_as_skipped_edge()<<"~"<<tedge->get_branch_distance_since_last_used()<<"]";
*output<<place<<"(r"<<start<<",r"<<stop<<","<<angle<<",\""<<label.str()<<"\",0.5);\n";
}
}
}
}
*output<<"endfig;\n";
string file = Settings_handle::st.get("mpost-graph-file").as<string>();
float width = (float)this->sequence->get_sites()->size()/(float)root_length;
*output2<<"\\includegraphics[width="<<width<<"\\columnwidth]{"<<file<<"."<<*count<<"}\n\n\\bigskip\n";
*output2<<"~\n\n\\bigskip\n";
++*count;
}
void Basic_alignment::check_skipped_boundaries(Sequence *sequence)
{
vector<Site> *sites = sequence->get_sites();
// First, find 'Match/Skipped' and 'Skipped/Matched' boundaries and update the counts
//
for(unsigned int i=0;i<sites->size();i++)
{
Site *tsite = &sites->at(i);
if( tsite->has_bwd_edge() )
{
Edge *edge = tsite->get_first_bwd_edge();
while( tsite->has_next_bwd_edge() )
{
Edge *another = tsite->get_next_bwd_edge();
if( another->get_start_site_index() > edge->get_start_site_index() )
edge = another;
}
Site *psite = &sites->at( edge->get_start_site_index() );
if( ( psite->get_path_state()==Site::matched || psite->get_path_state()==Site::start_site )
&& ( tsite->get_path_state()==Site::xskipped || tsite->get_path_state()==Site::yskipped ) )
{
edge->increase_branch_count_as_skipped_edge();
}
}
if( tsite->has_fwd_edge() )
{
Edge *edge = tsite->get_first_fwd_edge();
while( tsite->has_next_fwd_edge() )
{
Edge *another = tsite->get_next_fwd_edge();
if( another->get_start_site_index() < edge->get_start_site_index() )
edge = another;
}
Site *nsite = &sites->at( edge->get_end_site_index() );
if( ( tsite->get_path_state()==Site::xskipped || tsite->get_path_state()==Site::yskipped )
&& ( nsite->get_path_state()==Site::matched || nsite->get_path_state()==Site::ends_site ) )
{
edge->increase_branch_count_as_skipped_edge();
}
}
}
// Then, see if any pair of boundaries (covering a skipped gap) is above the limit. Delete the range.
//
bool non_skipped = true;
int skip_start = -1;
for(unsigned int i=1;i<sites->size();i++)
{
Site *tsite = &sites->at(i);
int tstate = tsite->get_path_state();
if( non_skipped && ( tstate == Site::xskipped || tstate == Site::yskipped ) )
{
if( tsite->has_bwd_edge() )
{
Edge *edge = tsite->get_first_bwd_edge();
while( tsite->has_next_bwd_edge() )
{
Edge *another = tsite->get_next_bwd_edge();
if( another->get_start_site_index() > edge->get_start_site_index() )
edge = another;
}
if(edge->get_branch_count_as_skipped_edge()>max_allowed_match_skip_branches)
{
skip_start = i;
}
}
non_skipped = false;
}
if(!non_skipped && skip_start>=0 && tstate == Site::matched)
{
int edge_ind = -1;
if( tsite->has_bwd_edge() )
{
Edge *edge = tsite->get_first_bwd_edge();
if(edge->get_branch_count_as_skipped_edge()>max_allowed_match_skip_branches)
edge_ind = edge->get_index();
while( tsite->has_next_bwd_edge() )
{
edge = tsite->get_next_bwd_edge();
if(edge->get_branch_count_as_skipped_edge()>max_allowed_match_skip_branches)
edge_ind = edge->get_index();
}
}
if(edge_ind>=0)
{
Log_output::write_out("Basic_alignemnmt: delete range: "+Log_output::itos(edge_ind)+" "+Log_output::itos(skip_start)+" "+Log_output::itos(i)+"\n",4);
this->delete_edge_range(sequence,edge_ind,skip_start);
}
non_skipped = true;
skip_start = -1;
}
if(tstate == Site::xgapped || tstate == Site::ygapped || tstate == Site::matched)
{
non_skipped = true;
skip_start = -1;
}
}
}
void Node::write_metapost_sequence_graph(ostream *output, ostream *output2, int *count, int root_length) const throw (Exception)
{
*output<<"beginfig("<<*count<<");\npickup pencircle scaled 1pt;\npath c[];\ndefaultscale := 0.5;\n";
vector<Site> *sites = this->sequence->get_sites();
string full_alphabet = this->sequence->get_full_alphabet();
stringstream all_chars;
for(unsigned int i=0;i<sites->size();i++)
{
Site *tsite = &sites->at(i);
char c = 's';
if(tsite->get_site_type()==Site::real_site)
c = full_alphabet.at(tsite->get_state());
else if(tsite->get_site_type()==Site::stop_site)
c = 'e';
string color = this->get_node_fill_color(c);
if(tsite->get_branch_count_since_last_used()>0)
color = "0.5white";
*output<<"c"<<i<<" = circle"<<"(("<<0.5*i<<"cm,0cm),\""<<c<<"\","<<color<<");\n";
}
if(leaf)
*output<<"label.top(btex $"<<this->get_name()<<"$ etex,(0.125cm,0.25cm));\n";
else
{
string n = this->get_name();
n = n.substr(1,n.length()-2);
*output<<"label.top(btex \\#"<<n<<"\\# etex,(0.125cm,0.25cm));\n";
}
*output<<"defaultscale := 0.25;\n";
for(unsigned int i=1;i<sites->size();i++)
{
Site *tsite = &sites->at(i);
if(tsite->has_bwd_edge())
{
Edge *tedge = tsite->get_first_bwd_edge();
int start = tedge->get_start_site_index();
int stop = tedge->get_end_site_index();
int angle = 0;
string place = "edgetop";
if(start+1==stop)
place = "edgebot";
else if(start+2==stop)
angle = 40;
else if(start+3==stop)
angle = 30;
else if(start+4<=stop)
angle = 20;
stringstream label;
if(tedge->get_branch_count_since_last_used()>0)
label<<"["<<tedge->get_branch_count_since_last_used()<<" "<<tedge->get_branch_count_as_skipped_edge()<<" "<<tedge->get_branch_distance_since_last_used()<<"]";
*output<<place<<"(c"<<start<<",c"<<stop<<","<<angle<<",\""<<label.str()<<"\",0.5);\n";
while(tsite->has_next_bwd_edge())
{
tedge = tsite->get_next_bwd_edge();
start = tedge->get_start_site_index();
stop = tedge->get_end_site_index();
angle = 0;
place = "edgetop";
if(start+1==stop)
place = "edgebot";
else if(start+2==stop)
angle = 40;
else if(start+3==stop)
angle = 30;
else if(start+4<=stop)
angle = 20;
label.str("");
if(tedge->get_branch_count_since_last_used()>0)
label<<"["<<tedge->get_branch_count_since_last_used()<<" "<<tedge->get_branch_count_as_skipped_edge()<<" "<<tedge->get_branch_distance_since_last_used()<<"]";
*output<<place<<"(c"<<start<<",c"<<stop<<","<<angle<<",\""<<label.str()<<"\",0.5);\n";
}
}
}
*output<<"endfig;\n";
string file = Settings_handle::st.get("mpost-graph-file").as<string>();
float width = (float)this->sequence->get_sites()->size()/(float)root_length;
*output2<<"\\includegraphics[width="<<width<<"\\columnwidth]{"<<file<<"."<<*count<<"}\n\n\\bigskip\n";
++*count;
}
void Basic_alignment::create_ancestral_edges(Sequence *sequence)
{
vector<Site> *sites = sequence->get_sites();
vector<int> left_child_index;
vector<int> right_child_index;
// First create an index for the child's sites in the parent
//
for(unsigned int i=0;i<sites->size();i++)
{
Site_children *offspring = sites->at(i).get_children();
Site *lsite;
Site *rsite;
if(offspring->left_index>=0)
{
lsite = left->get_site_at(offspring->left_index);
left_child_index.push_back(i);
}
if(offspring->right_index>=0)
{
rsite = right->get_site_at(offspring->right_index);
right_child_index.push_back(i);
}
}
if(Settings::noise>4)
{
stringstream ss;
ss<<"Child sequence site indeces:"<<endl;
for(unsigned int i=0;i<left_child_index.size();i++)
ss<<left_child_index.at(i)<<" ";
ss<<endl;
for(unsigned int i=0;i<right_child_index.size();i++)
ss<<right_child_index.at(i)<<" ";
ss<<endl;
Log_output::write_out(ss.str(),5);
}
// Then copy the edges of child sequences in their parent.
// Additionally, create edges for cases where skipped gap is flanked by a new gap.
//
Edge_history prev(-1,-1);
for(unsigned int i=1;i<sites->size();i++)
{
Site *psite = &sites->at(i);
int pstate = psite->get_path_state();
Site_children *offspring = psite->get_children();
// left sequence is matched
if(offspring->left_index>=0)
{
Site *tsite = left->get_site_at(offspring->left_index);
if( tsite->has_bwd_edge() )
{
Edge *child = tsite->get_first_bwd_edge();
this->transfer_child_edge(sequence, child, &left_child_index, left_branch_length );
while( tsite->has_next_bwd_edge() )
{
child = tsite->get_next_bwd_edge();
this->transfer_child_edge(sequence, child, &left_child_index, left_branch_length );
}
}
// these create edges to/from skipped sites flanked by gaps.
if( (pstate == Site::matched || pstate == Site::ends_site ) && prev.left_skip_site_index >= 0 && edges_for_skipped_flanked_by_gaps)
{
// edge from the skipped site to the *next* site
// as no better info is available, *this* edge is "copied" to one coming to the current site
Edge query(prev.left_skip_site_index,prev.left_skip_site_index+1);
int ind = left->get_fwd_edge_index_at_site(prev.left_skip_site_index,&query);
if(ind>=0)
{
Edge *child = &left->get_edges()->at(ind);
Edge edge( left_child_index.at(prev.left_skip_site_index), i );
this->transfer_child_edge(sequence, edge, child, left_branch_length );
}
prev.left_skip_site_index = -1;
}
else if(pstate == Site::xskipped && ( prev.path_state == Site::xgapped || prev.path_state == Site::ygapped ) && edges_for_skipped_flanked_by_gaps)
{
// the same here: use this as a template for an extra edge
Edge query(offspring->left_index-1, offspring->left_index);
int ind = left->get_bwd_edge_index_at_site(offspring->left_index,&query);
if(ind>=0)
{
Edge *child = &left->get_edges()->at(ind);
Edge edge( prev.match_site_index, i );
this->transfer_child_edge(sequence, edge, child, left_branch_length );
}
}
if((pstate == Site::xgapped || pstate == Site::xskipped )&& (prev.path_state == Site::ygapped || prev.path_state == Site::yskipped ))
{
Edge edge(i-1,i,1.0);
sequence->push_back_edge(edge);
sequence->get_site_at( edge.get_start_site_index() )->add_new_fwd_edge_index( sequence->get_current_edge_index() );
sequence->get_site_at( edge.get_end_site_index() )->add_new_bwd_edge_index( sequence->get_current_edge_index() );
}
if(pstate == Site::xskipped)
prev.left_skip_site_index = offspring->left_index;
else
prev.left_real_site_index = offspring->left_index;
if(pstate == Site::matched)
prev.match_site_index = i;
}
if(offspring->right_index>=0)
{
Site *tsite = right->get_site_at(offspring->right_index);
if( tsite->has_bwd_edge() )
{
Edge *child = tsite->get_first_bwd_edge();
this->transfer_child_edge(sequence, child, &right_child_index, right_branch_length );
while( tsite->has_next_bwd_edge() )
{
child = tsite->get_next_bwd_edge();
this->transfer_child_edge(sequence, child, &right_child_index, right_branch_length );
}
}
if( (pstate == Site::matched || pstate == Site::ends_site ) && prev.right_skip_site_index >= 0 && edges_for_skipped_flanked_by_gaps)
{
Edge query(prev.right_skip_site_index,prev.right_skip_site_index+1);
int ind = right->get_fwd_edge_index_at_site(prev.right_skip_site_index,&query);
if(ind>=0)
{
Edge *child = &right->get_edges()->at(ind);
Edge edge( right_child_index.at(prev.right_skip_site_index), i );
this->transfer_child_edge(sequence,edge, child, right_branch_length );
}
prev.right_skip_site_index = -1;
}
else if(pstate == Site::yskipped && ( prev.path_state == Site::xgapped || prev.path_state == Site::ygapped ) && edges_for_skipped_flanked_by_gaps)
{
Edge query(offspring->right_index-1, offspring->right_index);
int ind = right->get_bwd_edge_index_at_site(offspring->right_index,&query);
if(ind>=0)
{
Edge *child = &right->get_edges()->at(ind);
Edge edge( prev.match_site_index, i );
this->transfer_child_edge(sequence, edge, child, right_branch_length );
}
}
if((pstate == Site::ygapped || pstate == Site::yskipped) && (prev.path_state == Site::xgapped || prev.path_state == Site::xskipped))
{
Edge edge(i-1,i,1.0);
sequence->push_back_edge(edge);
sequence->get_site_at( edge.get_start_site_index() )->add_new_fwd_edge_index( sequence->get_current_edge_index() );
sequence->get_site_at( edge.get_end_site_index() )->add_new_bwd_edge_index( sequence->get_current_edge_index() );
}
if(pstate == Site::yskipped)
prev.right_skip_site_index = offspring->right_index;
else
prev.right_real_site_index = offspring->right_index;
}
prev.path_state = pstate;
}
}