예제 #1
0
파일: node.cpp 프로젝트: ajm/pagan-msa
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);
                }
            }
        }

    }
}
예제 #2
0
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;
        }
    }
}