GRAPH *create_graph(void){
GRAPH *temp=malloc(1*sizeof(GRAPH));
if(temp==NULL){
perror("MALLOC GRAPH");
exit(1);
}
temp->size=get_size_of_vertex();
temp->labels=create_points(temp);
temp->edges=alloc_edges(temp);
add_edges(temp);
view_edges(temp);
return temp;
}
// -----------------------------------------------------------------------------
// Draw all segments, ignoring connectivity.
// A segment is drawn if its segnum != -1.
void draw_mine_all(segment *sp, int automap_flag)
{
int s;
int i;
// clear visited list
for (i=0; i<=Highest_segment_index; i++)
Been_visited[i] = 0;
edge_list_size = min(Num_vertices*4,MAX_EDGES); //make maybe smaller than max
// clear edge list
for (i=0; i<edge_list_size; i++) {
edge_list[i].type = ET_EMPTY;
edge_list[i].face_count = 0;
edge_list[i].backface_count = 0;
}
n_used = 0;
for (s=0; s<=Highest_segment_index; s++)
if (sp[s].segnum != -1) {
for (i=0; i<MAX_SIDES_PER_SEGMENT; i++)
if (sp[s].sides[i].wall_num != -1)
draw_special_wall(&sp[s], i);
if (Search_mode)
check_segment(&sp[s]);
else {
add_edges(&sp[s]);
draw_seg_objects(&sp[s]);
}
}
draw_mine_edges(automap_flag);
}
InteractionGraph get_interaction_graph(ScoringFunctionAdaptor rsi,
const ParticlesTemp& ps) {
if (ps.empty()) return InteractionGraph();
InteractionGraph ret(ps.size());
Restraints rs= IMP::create_decomposition(rsi->create_restraints());
//Model *m= ps[0]->get_model();
IMP::base::map<ModelObject*, int> map;
InteractionGraphVertexName pm= boost::get(boost::vertex_name, ret);
DependencyGraph dg = get_dependency_graph(ps[0]->get_model());
DependencyGraphVertexIndex index= IMP::get_vertex_index(dg);
/*IMP_IF_LOG(VERBOSE) {
IMP_LOG_VERBOSE( "dependency graph is \n");
IMP::internal::show_as_graphviz(dg, std::cout);
}*/
for (unsigned int i=0; i< ps.size(); ++i) {
ParticlesTemp t= get_dependent_particles(ps[i],
ParticlesTemp(ps.begin(),
ps.end()),
dg, index);
for (unsigned int j=0; j< t.size(); ++j) {
IMP_USAGE_CHECK(map.find(t[j]) == map.end(),
"Currently particles which depend on more "
<< "than one particle "
<< "from the input set are not supported."
<< " Particle \"" << t[j]->get_name()
<< "\" depends on \"" << ps[i]->get_name()
<< "\" and \"" << ps[map.find(t[j])->second]->get_name()
<< "\"");
map[t[j]]= i;
}
IMP_IF_LOG(VERBOSE) {
IMP_LOG_VERBOSE( "Particle \"" << ps[i]->get_name() << "\" controls ");
for (unsigned int i=0; i< t.size(); ++i) {
IMP_LOG_VERBOSE( "\""<< t[i]->get_name() << "\" ");
}
IMP_LOG_VERBOSE( std::endl);
}
pm[i]= ps[i];
}
IMP::Restraints all_rs= IMP::get_restraints(rs);
for (Restraints::const_iterator it= all_rs.begin();
it != all_rs.end(); ++it) {
ModelObjectsTemp pl= (*it)->get_inputs();
add_edges(ps, pl, map, *it, ret);
}
/* Make sure that composite score states (eg the normalizer for
rigid body rotations) don't induce interactions among unconnected
particles.*/
ScoreStatesTemp ss= get_required_score_states(rs, dg, index);
for (ScoreStatesTemp::const_iterator it= ss.begin();
it != ss.end(); ++it) {
ModelObjectsTemps interactions=(*it)->get_interactions();
for (unsigned int i=0; i< interactions.size(); ++i) {
add_edges(ps, interactions[i], map, *it, ret);
}
}
IMP_INTERNAL_CHECK(boost::num_vertices(ret) == ps.size(),
"Wrong number of vertices "
<< boost::num_vertices(ret)
<< " vs " << ps.size());
return ret;
}
int maxcut_haplotyping(char* fragmentfile,char* variantfile,int snps,char* outputfile,int maxiter_hapcut)
{
// IMP NOTE: all SNPs start from 1 instead of 0 and all offsets are 1+
fprintf(stderr,"calling MAXCUT based haplotype assembly algorithm\n");
int fragments=0,iter=0,components=0; int i=0,j=0,k=0,t=0,component; int* slist; int flag =0;
float bestscore_mec = 0,calls=0, miscalls=0,ll = 0;
char buffer[MAXBUF];
/****************************** READ FRAGMENT MATRIX*************************************************/
struct fragment* Flist; FILE* ff = fopen(fragmentfile,"r");
if (ff == NULL) { fprintf(stderr,"couldn't open fragment file %s\n",fragmentfile); exit(0);}
fragments =0; while ( fgets(buffer,MAXBUF,ff) != NULL) fragments++; fclose(ff);
Flist = (struct fragment*)malloc(sizeof(struct fragment)*fragments);
flag = read_fragment_matrix(fragmentfile,Flist,fragments);
if (flag < 0) { fprintf(stderr,"unable to read fragment matrix file %s \n",fragmentfile); return -1; }
if (VCFformat ==0) snps = count_variants(variantfile);
else snps = count_variants_vcf(variantfile);
if (snps < 0) { fprintf(stderr,"unable to read variant file %s \n",variantfile); return -1; }
fprintf(stderr,"processed fragment file and variant file: fragments %d variants %d\n",fragments,snps);
/****************************** READ FRAGMENT MATRIX*************************************************/
struct SNPfrags* snpfrag = (struct SNPfrags*)malloc(sizeof(struct SNPfrags)*snps);
update_snpfrags(Flist,fragments,snpfrag,snps,&components);
double MEM_ALLOC = 0; for (i=0;i<snps;i++) MEM_ALLOC += snpfrag[i].edges*0.002; MEM_ALLOC *= 0.016;
fprintf(stderr,"%f MB memory needs to be allocated for graph edges\n",MEM_ALLOC); // size of struct edge is 16/1000 bytes
if (MEM_ALLOC >= MAX_MEMORY)
{
fprintf(stderr,"\nstoring the HAPCUT graph structure requires more than %d MB of memory:\n 1. increase the maximum memory available using option \"--maxmem 12000\" where the memory is specified in megabytes OR \n 2. run the program with the options \"--longreads 1 \" to reduce the number of edges stored \n\n",MAX_MEMORY);
return -1;
}
// too much memory allocated here for fosmid based data...
for (i=0;i<snps;i++) snpfrag[i].elist = (struct edge*)malloc(sizeof(struct edge)*snpfrag[i].edges);
for (i=0;i<snps;i++) snpfrag[i].telist = (struct edge*)malloc(sizeof(struct edge)*snpfrag[i].edges);
if (FOSMIDS ==0) add_edges(Flist,fragments,snpfrag,snps,&components);
else if (FOSMIDS >=1) add_edges_fosmids(Flist,fragments,snpfrag,snps,&components);
// this considers only components with at least two nodes
fprintf(stderr,"fragments %d snps %d component(blocks) %d\n",fragments,snps,components);
struct BLOCK* clist = (struct BLOCK*)malloc(sizeof(struct BLOCK)*components); component =0;
generate_clist_structure(Flist,fragments,snpfrag,snps,components,clist);
/*****************************************************************************************************/
char* HAP1 = (char*)malloc(snps+1); char* besthap_mec = (char*)malloc(snps+1);
char* HAP2 = (char*)malloc(snps+1);
struct tm *ts1; char buf[80]; time_t now;
slist = (int*)malloc(sizeof(int)*snps); char fn[1000];
if (VCFformat ==0) read_variantfile(variantfile,snpfrag,snps); else read_vcffile(variantfile,snpfrag,snps);
/*****************************************************************************************************/
if (RANDOM_START ==1)
{
fprintf(stdout,"starting from a completely random solution SOLUTION \n");
for (i=0;i<snps;i++)
{
if (snpfrag[i].frags ==0) { HAP1[i] = '-'; HAP2[i] = '-'; }
else
{
if (drand48() < 0.5) { HAP1[i] = '0'; HAP2[i] = '1'; } else {HAP1[i] = '1'; HAP2[i] = '0'; }
}
}
}
for (i=0;i<snps;i++) { besthap_mec[i] = HAP1[i]; }
// for each block, we maintain best haplotype solution under MFR criterion
// compute the component-wise score for 'initHAP' haplotype
miscalls=0;bestscore_mec=0;
for (k=0;k<components;k++)
{
clist[k].MEC =0; clist[k].bestMEC =0; clist[k].calls =0; clist[k].LL = 0;
for (i=0;i<clist[k].frags;i++)
{
update_fragscore(Flist,clist[k].flist[i],HAP1); clist[k].MEC += Flist[clist[k].flist[i]].currscore;
clist[k].LL += Flist[clist[k].flist[i]].ll; clist[k].calls += Flist[clist[k].flist[i]].calls;
}
clist[k].bestMEC = clist[k].MEC; bestscore_mec += clist[k].bestMEC; miscalls += clist[k].MEC; clist[k].bestLL = clist[k].LL;
}
// annealing_haplotyping(Flist,fragments,snpfrag,snps,maxiter,HAP1,HAP2,clist,components,slist); return 1;
// annealing_haplotyping_full(Flist,fragments,snpfrag,snps,maxiter,HAP1,HAP2,0); return 1;
/************************** RUN THE MAX_CUT ALGORITHM ITERATIVELY TO IMPROVE MEC SCORE*********************************/
for (iter=0;iter<maxiter_hapcut;iter++)
{
mecscore(Flist,fragments,HAP1,&ll,&calls,&miscalls);
time(&now); ts1 = localtime(&now); strftime(buf, sizeof(buf), "%a %Y-%m-%d %H:%M:%S %Z", ts1);
fprintf(stdout,"iter %d current haplotype MEC %f calls %d LL %f %s \n",iter,miscalls,(int)calls,ll,buf);
fprintf(stderr,"iter %d current haplotype MEC %f calls %d LL %f %s \n",iter,miscalls,(int)calls,ll,buf);
if ((iter%10==0 && iter > 0))
{
// new code added april 7 2012
for (k=0;k<components;k++) find_bestvariant_segment(Flist,fragments,snpfrag,clist,k,HAP1,HAP2);
sprintf(fn,"%s",outputfile); // newfile for every update to score....
//sprintf(fn,"%s.%f",outputfile,miscalls); // newfile for every update to score....
fprintf(stdout,"OUTPUTTING HAPLOTYPE ASSEMBLY TO FILE %s\n",fn); fprintf(stderr,"OUTPUTTING HAPLOTYPE ASSEMBLY TO FILE %s\n",fn);
//if (VCFformat ==1) print_haplotypes_vcf(clist,components,HAP1,Flist,fragments,snpfrag,snps,fn);
print_hapfile(clist,components,HAP1,Flist,fragments,snpfrag,variantfile,miscalls,fn);
// do this only if some option is specified
if (PRINT_FRAGMENT_SCORES ==1)
{
print_fragmentmatrix_MEC(Flist,fragments,HAP1,outputfile);
//print_matrix(clist,components,HAP1,Flist,outputfile);
}
}
for (k=0;k<components;k++) // COMPUTATION OF TREE FOR EACH COMPONENT
{
//if ((k*50)%components ==0) fprintf(stderr,"#");
if (iter ==0) fprintf(stdout,"\n component %d length %d phased %d %d...%d \n",k,clist[k].length,clist[k].phased,clist[k].offset,clist[k].lastvar);
// call function for each component only if MEC > 0 april 17 2012
if (clist[k].MEC > 0) evaluate_cut_component(Flist,snpfrag,clist,k,slist,HAP1,iter);
}
for (i=0;i<snps;i++)
{
// commented out on april 6 4pm 2012
//if (HAP1[i] == '0') HAP2[i] = '1'; else if (HAP1[i] == '1') HAP2[i] = '0'; else HAP2[i] = HAP1[i];
}
}
/************************** RUN THE MAX_CUT ALGORITHM ITERATIVELY TO IMPROVE MEC SCORE*********************************/
// annealing_haplotyping_full(Flist,fragments,snpfrag,snps,maxiter+100,HAP1,HAP2,0); return 1;
return 1;
}
void edges(std::initializer_list<std::initializer_list<int>> pairs) {
clear();
add_edges(pairs);
}
adjacency_matrix(std::initializer_list<std::initializer_list<int>> pairs, std::size_t nodes_count, bool directed = false) :
adjacency_matrix{nodes_count, directed}
{
add_edges(pairs);
}
int maxcut_haplotyping(char* fragmentfile, char* variantfile, char* outputfile) {
// IMP NOTE: all SNPs start from 1 instead of 0 and all offsets are 1+
fprintf_time(stderr, "Calling Max-Likelihood-Cut based haplotype assembly algorithm\n");
int snps = 0;
int fragments = 0, iter = 0, components = 0;
int i = 0, k = 0;
int* slist;
int flag = 0;
float bestscore = 0, miscalls = 0;
int hic_iter=0;
struct SNPfrags* snpfrag = NULL;
struct BLOCK* clist;
char* HAP1;
float HIC_LL_SCORE = -80;
float OLD_HIC_LL_SCORE = -80;
int converged_count=0, split_count, new_components, component;
int new_fragments = 0;
struct fragment* new_Flist;
// READ FRAGMENT MATRIX
fragments = get_num_fragments(fragmentfile);
struct fragment* Flist;
Flist = (struct fragment*) malloc(sizeof (struct fragment)* fragments);
flag = read_fragment_matrix(fragmentfile, Flist, fragments);
if (MAX_IS != -1){
// we are going to filter out some insert sizes
new_fragments = 0;
new_Flist = (struct fragment*) malloc(sizeof (struct fragment)* fragments);
for(i = 0; i < fragments; i++){
if (Flist[i].isize < MAX_IS) new_Flist[new_fragments++] = Flist[i];
}
Flist = new_Flist;
fragments = new_fragments;
}
if (flag < 0) {
fprintf_time(stderr, "unable to read fragment matrix file %s \n", fragmentfile);
return -1;
}
//ADD EDGES BETWEEN SNPS
snps = count_variants_vcf(variantfile);
if (snps < 0) {
fprintf_time(stderr, "unable to read variant file %s \n", variantfile);
return -1;
}
snpfrag = (struct SNPfrags*) malloc(sizeof (struct SNPfrags)*snps);
update_snpfrags(Flist, fragments, snpfrag, snps, &components);
detect_long_reads(Flist,fragments);
// 10/25/2014, edges are only added between adjacent nodes in each fragment and used for determining connected components...
for (i = 0; i < snps; i++) snpfrag[i].elist = (struct edge*) malloc(sizeof (struct edge)*(snpfrag[i].edges+1));
if (LONG_READS ==0){
add_edges(Flist,fragments,snpfrag,snps,&components);
}else if (LONG_READS >=1){
add_edges_fosmids(Flist,fragments,snpfrag,snps,&components);
}
for (i = 0; i < snps; i++) snpfrag[i].telist = (struct edge*) malloc(sizeof (struct edge)*(snpfrag[i].edges+1));
// this considers only components with at least two nodes
fprintf_time(stderr, "fragments %d snps %d component(blocks) %d\n", fragments, snps, components);
// BUILD COMPONENT LIST
clist = (struct BLOCK*) malloc(sizeof (struct BLOCK)*components);
generate_clist_structure(Flist, fragments, snpfrag, snps, components, clist);
// READ VCF FILE
read_vcffile(variantfile, snpfrag, snps);
// INITIALIZE RANDOM HAPLOTYPES
HAP1 = (char*) malloc(snps + 1);
for (i = 0; i < snps; i++) {
if (snpfrag[i].frags == 0 || (SNVS_BEFORE_INDELS && (strlen(snpfrag[i].allele0) != 1 || strlen(snpfrag[i].allele1) != 1))) {
HAP1[i] = '-';
} else if (drand48() < 0.5) {
HAP1[i] = '0';
} else {
HAP1[i] = '1';
}
}
// for each block, we maintain best haplotype solution under MFR criterion
// compute the component-wise score for 'initHAP' haplotype
miscalls = 0;
bestscore = 0;
for (k = 0; k < components; k++) {
clist[k].SCORE = 0;
clist[k].bestSCORE = 0;
for (i = 0; i < clist[k].frags; i++) {
update_fragscore(Flist, clist[k].flist[i], HAP1);
clist[k].SCORE += Flist[clist[k].flist[i]].currscore;
}
clist[k].bestSCORE = clist[k].SCORE;
bestscore += clist[k].bestSCORE;
miscalls += clist[k].SCORE;
}
fprintf_time(stderr, "processed fragment file and variant file: fragments %d variants %d\n", fragments, snps);
int MAXIS = -1;
if (HIC){
// determine the probability of an h-trans interaction for read
for (i=0; i<fragments;i++){
Flist[i].htrans_prob = -80;
if (Flist[i].isize > MAXIS)
MAXIS = Flist[i].isize;
}
HTRANS_MAXBINS = MAXIS/HTRANS_BINSIZE + 1;
}else{
HTRANS_MAXBINS = 0;
}
// read in file with estimated probabilities of Hi-C h-trans interactions with distance
if (strcmp(HTRANS_DATA_INFILE, "None") != 0){
int num_bins = count_htrans_bins(HTRANS_DATA_INFILE);
float* htrans_probs = (float*) malloc(sizeof(float) * num_bins);
read_htrans_file(HTRANS_DATA_INFILE, htrans_probs, num_bins);
for (i=0; i<fragments;i++){
Flist[i].htrans_prob = log10(htrans_probs[Flist[i].isize / HTRANS_BINSIZE]);
}
free(htrans_probs);
}
slist = (int*) malloc(sizeof (int)*snps);
OLD_HIC_LL_SCORE = bestscore;
for (hic_iter = 0; hic_iter < MAX_HIC_EM_ITER; hic_iter++){
if (VERBOSE)
fprintf_time(stdout, "HIC ITER %d\n", hic_iter);
for (k = 0; k < components; k++){
clist[k].iters_since_improvement = 0;
}
for (i=0; i<snps; i++){
snpfrag[i].post_hap = 0;
}
// RUN THE MAX_CUT ALGORITHM ITERATIVELY TO IMPROVE LIKELIHOOD
for (iter = 0; iter < MAXITER; iter++) {
if (VERBOSE)
fprintf_time(stdout, "PHASING ITER %d\n", iter);
converged_count = 0;
for (k = 0; k < components; k++){
if(VERBOSE && iter == 0)
fprintf_time(stdout, "component %d length %d phased %d %d...%d\n", k, clist[k].length, clist[k].phased, clist[k].offset, clist[k].lastvar);
if (clist[k].SCORE > 0)
converged_count += evaluate_cut_component(Flist, snpfrag, clist, k, slist, HAP1);
else converged_count++;
}
if (converged_count == components) {
//fprintf(stdout, "Haplotype assembly terminated early because no improvement seen in blocks after %d iterations\n", CONVERGE);
break;
}
}
// H-TRANS ESTIMATION FOR HIC
if (MAX_HIC_EM_ITER > 1){
// Possibly break if we're done improving
HIC_LL_SCORE = 0;
for (k = 0; k < components; k++){
HIC_LL_SCORE += clist[k].bestSCORE;
}
if (HIC_LL_SCORE >= OLD_HIC_LL_SCORE){
break;
}
OLD_HIC_LL_SCORE = HIC_LL_SCORE;
likelihood_pruning(snps, Flist, snpfrag, HAP1, 0); // prune for only very high confidence SNPs
// estimate the h-trans probabilities for the next round
estimate_htrans_probs(Flist, fragments, HAP1, snpfrag);
}
}
// BLOCK SPLITTING
new_components = components;
if (SPLIT_BLOCKS){
split_count = 0;
for (k=0; k<components; k++){
// attempt to split block
split_count += split_block(HAP1, clist, k, Flist, snpfrag, &new_components);
}
if (split_count > 0){
// regenerate clist if necessary
free(clist);
clist = (struct BLOCK*) malloc(sizeof (struct BLOCK)*new_components);
generate_clist_structure(Flist, fragments, snpfrag, snps, new_components, clist);
}
components = new_components;
}else if(ERROR_ANALYSIS_MODE && !HIC){
for (k=0; k<components; k++){
// run split_block but don't actually split, just get posterior probabilities
split_block(HAP1, clist, k, Flist, snpfrag, &new_components);
}
}
// PRUNE SNPS
if (!SKIP_PRUNE){
discrete_pruning(snps, fragments, Flist, snpfrag, HAP1);
likelihood_pruning(snps, Flist, snpfrag, HAP1, CALL_HOMOZYGOUS);
}
// PRINT OUTPUT FILE
fprintf_time(stderr, "OUTPUTTING PRUNED HAPLOTYPE ASSEMBLY TO FILE %s\n", outputfile);
print_hapfile(clist, components, HAP1, Flist, fragments, snpfrag, variantfile, miscalls, outputfile);
char assignfile[4096]; sprintf(assignfile,"%s.fragments",outputfile);
if (OUTPUT_RH_ASSIGNMENTS ==1) fragment_assignments(Flist,fragments,snpfrag,HAP1,assignfile); // added 03/10/2018 to output read-haplotype assignments
char outvcffile[4096]; sprintf(outvcffile,"%s.phased.VCF",outputfile);
if (OUTPUT_VCF ==1) {
fprintf_time(stderr, "OUTPUTTING PHASED VCF TO FILE %s\n", outvcffile);
output_vcf(variantfile,snpfrag,snps,HAP1,Flist,fragments,outvcffile,0);
}
// FREE UP MEMORY
for (i = 0; i < snps; i++) free(snpfrag[i].elist);
for (i = 0; i < snps; i++) free(snpfrag[i].telist);
component = 0;
for (i = 0; i < snps; i++) {
free(snpfrag[i].flist);
free(snpfrag[i].alist);
free(snpfrag[i].jlist);
free(snpfrag[i].klist);
if (snpfrag[i].component == i && snpfrag[i].csize > 1) // root node of component
{
free(clist[component].slist);
component++;
}
}
for (i = 0; i < components; i++) free(clist[i].flist);
free(snpfrag);
free(clist);
free(Flist);
return 0;
}
bool
RoutePlanner::solve(const AGeoPoint& origin,
const AGeoPoint& destination,
const RoutePlannerConfig& config,
const short h_ceiling)
{
on_solve(origin, destination);
rpolars_route.set_config(config, std::max(destination.altitude, origin.altitude),
h_ceiling);
rpolars_reach.set_config(config, std::max(destination.altitude, origin.altitude),
h_ceiling);
m_reach_polar_mode = config.reach_polar_mode;
{
const AFlatGeoPoint s_origin(task_projection.project(origin), origin.altitude);
const AFlatGeoPoint s_destination(task_projection.project(destination), destination.altitude);
if (!(s_origin == origin_last) || !(s_destination == destination_last))
dirty = true;
if (is_trivial())
return false;
dirty = false;
origin_last = s_origin;
destination_last = s_destination;
h_min = std::min(s_origin.altitude, s_destination.altitude);
h_max = rpolars_route.cruise_altitude;
}
solution_route.clear();
solution_route.push_back(origin);
solution_route.push_back(destination);
if (!rpolars_route.terrain_enabled() && !rpolars_route.airspace_enabled())
return false; // trivial
m_search_hull.clear();
m_search_hull.push_back(SearchPoint(origin_last, task_projection));
RoutePoint start = origin_last;
m_astar_goal = destination_last;
RouteLink e_test(start, m_astar_goal, task_projection);
if (e_test.is_short())
return false;
if (!rpolars_route.achievable(e_test))
return false;
count_dij=0;
count_airspace=0;
count_terrain=0;
count_supressed=0;
bool retval = false;
m_planner.restart(start);
unsigned best_d = UINT_MAX;
if (verbose) {
printf("# goal node (%d,%d,%d)\n",
m_astar_goal.Longitude, m_astar_goal.Latitude, m_astar_goal.altitude);
printf("# start node (%d,%d,%d)\n",
start.Longitude, start.Latitude, start.altitude);
}
while (!m_planner.empty()) {
const RoutePoint node = m_planner.pop();
if (verbose>1) {
printf("# processing node (%d,%d,%d) %d,%d q size %d\n",
node.Longitude, node.Latitude, node.altitude,
m_planner.get_node_value(node).g,
m_planner.get_node_value(node).h,
m_planner.queue_size());
}
h_min = std::min(h_min, node.altitude);
h_max = std::max(h_max, node.altitude);
bool is_final = (node == m_astar_goal);
if (is_final) {
if (!retval)
best_d = UINT_MAX;
retval = true;
}
if (is_final) // @todo: allow fallback if failed
{ // copy improving solutions
Route this_solution;
unsigned d = find_solution(node, this_solution);
if (d< best_d) {
best_d = d;
solution_route = this_solution;
}
}
if (retval)
break; // want top solution only
// shoot for final
RouteLink e(node, m_astar_goal, task_projection);
if (set_unique(e))
add_edges(e);
while (!m_links.empty()) {
add_edges(m_links.front());
m_links.pop();
}
}
count_unique = m_unique.size();
if (retval && verbose) {
printf("# solved with %d intermediate points\n", (int)(solution_route.size()-2));
}
if (retval) {
// correct solution for rounding
assert(solution_route.size()>=2);
for (unsigned i=0; i< solution_route.size(); ++i) {
FlatGeoPoint p(task_projection.project(solution_route[i]));
if (p== origin_last) {
solution_route[i] = AGeoPoint(origin, solution_route[i].altitude);
} else if (p== destination_last) {
solution_route[i] = AGeoPoint(destination, solution_route[i].altitude);
}
}
} else {
solution_route.clear();
solution_route.push_back(origin);
solution_route.push_back(destination);
}
m_planner.clear();
m_unique.clear();
// m_search_hull.clear();
return retval;
}
