satcheck_smvsatt::satcheck_smvsatt()
{
satsolver=
sat_instance_new_type(SATSOLVERCORE1, no_variables(), true);
// now we can do l_const
init_const();
}
int
neighborj_score_string ( const char *constTree,
struct genome_struct *genome_list, int num_genes,
int num_genomes,
distmem_t * distmem, int CIRCULAR,
struct tNode *tpool, int *edgepool,
struct genome_struct *labels,
int initmethod, int COND,
struct qNode *qpool,
struct adj_struct *adj_list,
struct adj_struct *adj_pool,
int *stack, int *degree, int *otherEnd,
intpair_t * neighbors,
smalledge_t * smalledges,
edge_t * edges,
int *outcycle, int *pred1, int *pred2, int *picked,
int *decode, int inittspsolver,
triple_t * triple, int *incycle, int tspsolver,
int distmethod,
int thresh, int **weights, int **status,
int *best_so_far, env_t * const_env,
int *genes,
int *condense_succ, int *condense_decode,
int orig_num_genes, int correction,
char *treeString )
{
int score;
ConstraintTree_T const_tree;
struct tNode *tree;
int index;
int i;
#ifdef DEBUG
fprintf ( outfile, "Neighbor-Joining Tree: %s\n\n", constTree );
fflush ( outfile );
#endif
init_const ( const_env, constTree, const_tree, tpool );
tree = first_const ( const_tree, tpool, 0, const_env );
#ifdef DEBUG
print_tree_tag ( tree );
#endif
tree->leaf = TRUE;
index = 0;
SetTreeEdgePtrs ( tree, edgepool, &index );
for ( i = 0; i < 2 * num_genomes + 6; i++ )
{
tpool[i].genome = NULL;
}
add_genomes_to_tree ( tree, labels, genome_list, num_genes );
switch ( initmethod )
{
case RAND:
initialize_tree_random ( tree, labels, num_genes, num_genomes );
break;
case SMALLNN:
initialize_tree_SNN ( COND, tree, tpool, labels, qpool, adj_list,
adj_pool, weights, stack, degree, otherEnd,
neighbors, edges, incycle, outcycle, pred1,
pred2, picked, decode, num_genes,
num_genomes, inittspsolver, thresh,
CIRCULAR );
/* reuses pred1, pred2, picked */
break;
case SBNN:
initialize_tree_SBNN ( COND, tree, tpool, labels, qpool, adj_list,
adj_pool, weights, stack, degree, otherEnd,
neighbors, edges, incycle, outcycle, pred1,
pred2, picked, decode, num_genes,
num_genomes, inittspsolver, thresh,
CIRCULAR );
/* reuses pred1, pred2, picked */
break;
case BIGNN:
initialize_tree_BNN ( COND, tree, tpool, labels, triple, adj_list,
adj_pool, weights, stack, degree, otherEnd,
neighbors, edges, incycle, outcycle, pred1,
pred2, picked, decode, num_genes,
num_genomes, inittspsolver, thresh,
CIRCULAR );
/* reuses pred1, pred2, picked */
break;
case FASTPROP:
initialize_tree_propagate ( COND, tree, tpool, labels, qpool,
adj_list, adj_pool, weights, stack,
degree, otherEnd, neighbors, edges,
incycle, outcycle, num_genes,
num_genomes, pred1, pred2, picked,
decode, FAST, tspsolver, thresh,
CIRCULAR );
break;
case MEDIANPROP:
initialize_tree_propagate ( COND, tree, tpool, labels, qpool,
adj_list, adj_pool, weights, stack,
degree, otherEnd, neighbors, edges,
incycle, outcycle, num_genes,
num_genomes, pred1, pred2, picked,
decode, MEDIAN, inittspsolver, thresh,
CIRCULAR );
break;
case TRIV:
initialize_tree_trivial ( tree, labels, num_genes, num_genomes );
break;
case ADJPARS:
initialize_tree_adjpars ( tree, tpool, labels,
stack, degree, otherEnd, neighbors,
smalledges, incycle, outcycle,
num_genes, num_genomes, weights, status,
inittspsolver, thresh, CIRCULAR );
break;
default:
fprintf ( stderr, "ERROR: no initialization given\n" );
}
score =
score_tree ( tree, num_genes, CIRCULAR, distmethod, distmem,
correction );
#ifdef DEBUG
fprintf ( outfile, "initial score=%5d\n", score );
fflush ( outfile );
#endif
score =
iterate_over_tree ( COND, tree, num_genes, num_genomes, tspsolver,
thresh, score, adj_list, adj_pool, neighbors,
stack, incycle, outcycle, weights, degree,
otherEnd, edges, tpool, labels, pred1, pred2,
picked, decode, genes, CIRCULAR, distmethod,
distmem, correction );
if ( score < *best_so_far )
{
*best_so_far = score;
#ifdef MPBPA
if ( MYPROC == 0 )
{
#endif
fprintf ( outfile, "Neighbor-Joining Tree: %s\n\n", constTree );
fflush ( outfile );
switch ( distmethod )
{
case DIST_BP:
fprintf ( outfile, "NJ breakpoint score = %12d\n",
score );
fprintf ( outfile, "NJ inversion score = %12d\n",
score_tree ( tree, num_genes, CIRCULAR,
DIST_INV, distmem, correction ) );
fflush ( outfile );
break;
case DIST_INV:
fprintf ( outfile, "NJ inversion score = %12d\n",
score );
fprintf ( outfile, "NJ breakpoint score = %12d\n",
score_tree ( tree, num_genes, CIRCULAR, DIST_BP,
distmem, correction ) );
fflush ( outfile );
break;
}
#ifdef DEBUG
print_tree_tag ( tree );
#endif
print_tree_uncondensed ( tree, num_genes,
condense_succ, condense_decode,
orig_num_genes );
if ( treeString != NULL )
print_tree_nexus_noscore ( treeString, tree );
fprintf ( outfile, "\n" );
/* testing */
#ifdef MPBPA
}
#endif
}
return ( score );
}