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labeltree.c
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labeltree.c
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#include "structs.h"
#include "labeltree.h"
#include "convert.h"
#include "lk_main.h"
#include "bbtsp.h"
#include "binencode.h"
#include "invdist.h"
#include "condense3.h"
#include "cheaptsp.h"
#include "inversion_median.h"
#include "inversion_median_alberto.h"
#include "correction.h"
#include "inversion_median.h"
#include "sorting_reversal_median.h"
extern int VIncrease;
void
printedgescores ( struct tNode *tree )
{
if ( tree == NULL )
return;
if ( tree->lChild )
{
fprintf ( outfile, "tree_score: edge %p is worth %4d\n",
tree->sc_lChild, *( tree->sc_lChild ) );
fflush ( outfile );
printedgescores ( tree->lChild );
}
if ( tree->rChild )
{
fprintf ( outfile, "tree_score: edge %p is worth %4d\n",
tree->sc_rChild, *( tree->sc_rChild ) );
fflush ( outfile );
printedgescores ( tree->rChild );
}
return;
}
int
iterate_over_tree ( int COND, struct tNode *tree, int num_genes,
int num_genomes, int tspsolver, int thresh, int score,
struct adj_struct *adj_list, struct adj_struct *adj_pool,
intpair_t * neighbors, int *stack, int *incycle,
int *outcycle, int **weights, int *degree, int *otherEnd,
edge_t * edges, struct tNode *tpool,
struct genome_struct *labels, int *pred1, int *pred2,
int *picked, int *decode, int *genes, int CIRCULAR,
int distmethod, distmem_t * distmem, int correction )
{
int best_so_far = score;
struct tNode *condnode1 = NULL, *condnode2 = NULL, *condnode3 =
NULL, *condmedian = NULL;
int IMPROVED = TRUE;
int ncount;
int relabel = 0;
VIncrease = 100;
#ifdef DEBUG
fprintf ( outfile, "before assigning condnodes\n" );
printedgescores ( tree );
#endif
if ( COND )
{
ncount = 2 * num_genomes;
condnode1 = &tpool[ncount + 2];
condnode1->genome = &labels[ncount + 2];
condnode2 = &tpool[ncount + 3];
condnode2->genome = &labels[ncount + 3];
condnode3 = &tpool[ncount + 4];
condnode3->genome = &labels[ncount + 4];
condmedian = &tpool[ncount + 5];
condmedian->genome = &labels[ncount + 5];
}
#ifdef DEBUG
fprintf ( outfile, "after assigning condnodes\n" );
printedgescores ( tree );
#endif
while ( IMPROVED )
{
IMPROVED = FALSE;
init_change_bits ( tree );
dfs_label_tree ( COND, tree, tree, &best_so_far, &IMPROVED,
num_genes, num_genomes, weights, &relabel, tspsolver,
thresh, adj_list, adj_pool, neighbors, stack,
incycle, outcycle, degree, otherEnd, edges, tpool,
labels, pred1 + num_genes, pred2 + num_genes,
picked + num_genes, decode,
/* the num_genes offsets to allow negative indexing */
condmedian, condnode1, condnode2, condnode3,
genes, CIRCULAR, distmethod, distmem, correction );
leaf_tree ( tree ); /* reset visited flag */
}
#ifdef PRINT
printf ( "relabeled %d nodes, tree score: %d\n", relabel, best_so_far );
#endif
return ( best_so_far );
}
/* must define exactly one of PREORDER or POSTORDER --- NOT BOTH!!! */
#define POSTORDER
void
dfs_label_tree ( int COND, struct tNode *root, struct tNode *tree_node,
int *best_so_far, int *IMPROVED,
int num_genes, int num_genomes,
int **weights, int *relabel,
int tspsolver, int thresh,
struct adj_struct *adj_list, struct adj_struct *adj_pool,
intpair_t * neighbors, int *stack, int *incycle,
int *outcycle, int *degree, int *otherEnd, edge_t * edges,
struct tNode *tpool, struct genome_struct *labels, int *pred,
int *succ, int *code, int *decode,
/* pred, succ, and code have middle ptrs! */
struct tNode *condmedian, struct tNode *condnode1,
struct tNode *condnode2, struct tNode *condnode3,
int *genes, int CIRCULAR,
int distmethod, distmem_t * distmem, int correction )
{
int score = 0, delta;
int i, num_cond;
int realsolver, same, use_median = TRUE;
struct genome_struct *pargenome, *lchgenome, *rchgenome;
struct genome_struct *gen[3];
int tmp_sc_parent = 0, tmp_sc_lChild = 0, tmp_sc_rChild = 0;
if ( tree_node == NULL )
return;
#ifdef POSTORDER
if ( !tree_node->lChild->leaf )
{
dfs_label_tree ( COND, root, tree_node->lChild, best_so_far, IMPROVED,
num_genes, num_genomes, weights, relabel, tspsolver,
thresh, adj_list, adj_pool, neighbors, stack,
incycle, outcycle, degree, otherEnd, edges, tpool,
labels, pred, succ, code, decode, condmedian,
condnode1, condnode2, condnode3, genes, CIRCULAR,
distmethod, distmem, correction );
}
if ( tree_node->rChild )
{
if ( !tree_node->rChild->leaf )
{
dfs_label_tree ( COND, root, tree_node->rChild, best_so_far,
IMPROVED, num_genes, num_genomes, weights,
relabel, tspsolver, thresh, adj_list, adj_pool,
neighbors, stack, incycle, outcycle, degree,
otherEnd, edges, tpool, labels, pred, succ, code,
decode, condmedian, condnode1, condnode2,
condnode3, genes, CIRCULAR, distmethod, distmem,
correction );
}
}
#endif
if ( tree_node->need_change > 0 )
{ /* internal node needs to be relabeled */
if ( COND )
{ /* condensation */
for ( i = 0; i < num_genes; i++ )
{ /* save old label */
genes[i] = tree_node->genome->genes[i];
}
pargenome = tree_node->parent->genome;
lchgenome = tree_node->lChild->genome;
rchgenome = tree_node->rChild->genome;
#ifdef DEBUG
fprintf ( outfile, "ptrs to old edge scores are %p, %p, and %p\n",
tree_node->sc_parent,
tree_node->sc_lChild, tree_node->sc_rChild );
fprintf ( outfile, "old edge scores are %3d, %3d, and %3d\n",
*( tree_node->sc_parent ),
*( tree_node->sc_lChild ), *( tree_node->sc_rChild ) );
fflush ( outfile );
#endif
condense3 ( pargenome->genes, lchgenome->genes, rchgenome->genes,
condnode1->genome->genes, condnode2->genome->genes,
condnode3->genome->genes,
num_genes, &num_cond, succ, pred, code, decode );
if ( num_cond == 0 )
{ /* three identical neighbors... */
/* note: only works for circular genome; for linear, value is 1 */
for ( i = 0; i < num_genes; i++ )
{ /* so just copy on in place */
tree_node->genome->genes[i] =
tree_node->parent->genome->genes[i];
}
tree_node->need_change = 0;
goto done; /* and exit */
}
/* call solvers with condensed genomes */
/* the LK solvers need a weight matrix, but the bbtsp solver does not */
/* force use of bbtsp if problem is too small */
realsolver = tspsolver;
if ( ( num_cond <= thresh ) && ( tspsolver != TSP_COALESCED ) )
realsolver = TSP_BBTSP;
switch ( realsolver )
{
case INVERSION_MEDIAN:
gen[0] = condnode1->genome;
gen[1] = condnode2->genome;
gen[2] = condnode3->genome;
find_reversal_median ( condmedian->genome, gen, num_cond,
NULL );
/*find_inversion_median(condmedian->genome, gen, num_cond, distmem); */
if ( CIRCULAR )
{
score += invdist_circular ( gen[0],
condmedian->genome,
num_cond, distmem );
score +=
invdist_circular ( gen[1], condmedian->genome,
num_cond, distmem );
score +=
invdist_circular ( gen[2], condmedian->genome,
num_cond, distmem );
}
else
{
score += invdist_noncircular ( gen[0],
condmedian->genome, 0,
num_cond, distmem );
score +=
invdist_noncircular ( gen[1], condmedian->genome,
0, num_cond, distmem );
score +=
invdist_noncircular ( gen[2], condmedian->genome,
0, num_cond, distmem );
}
break;
case INVERSION_MEDIAN_FAST:
gen[0] = condnode1->genome;
gen[1] = condnode2->genome;
gen[2] = condnode3->genome;
score = 0;
if ( CIRCULAR )
{
albert_inversion_median_circular ( gen, num_cond,
condmedian->
genome->genes );
score +=
invdist_circular ( gen[0], condmedian->genome,
num_cond, distmem );
score +=
invdist_circular ( gen[1], condmedian->genome,
num_cond, distmem );
score +=
invdist_circular ( gen[2], condmedian->genome,
num_cond, distmem );
}
else
{
albert_inversion_median_noncircular ( gen, num_cond,
condmedian->
genome->genes );
score +=
invdist_noncircular ( gen[0], condmedian->genome,
0, num_cond, distmem );
score +=
invdist_noncircular ( gen[1], condmedian->genome,
0, num_cond, distmem );
score +=
invdist_noncircular ( gen[2], condmedian->genome,
0, num_cond, distmem );
}
break;
case TSP_BBTSP:
/* does not create a weight matrix, but sets weight in the adj lists */
convert2_to_tsp ( condnode1->genome, condnode2->genome,
condnode3->genome, adj_list, adj_pool,
num_cond, CIRCULAR );
score = bbtsp ( 2 * num_cond, condmedian->genome->genes, FALSE, /* cannot use median that does not exist */
condnode1->genome->genes,
condnode2->genome->genes,
condnode3->genome->genes, adj_list,
neighbors, stack, outcycle, degree,
otherEnd, edges, CIRCULAR );
break;
#ifdef CONCORDE
case TSP_CHLINKERN:
/* creates a weight matrix -- more expensive! */
convert_to_tsp ( condnode1->genome, condnode2->genome,
condnode3->genome, num_cond, CIRCULAR,
weights );
score =
chlinkern ( 2 * num_cond, weights,
condmedian->genome->genes, incycle,
outcycle );
break;
case TSP_GREEDYLK:
/* creates a weight matrix -- more expensive! */
convert_to_tsp ( condnode1->genome, condnode2->genome,
condnode3->genome, num_cond, CIRCULAR,
weights );
score =
greedylk ( 2 * num_cond, weights,
condmedian->genome->genes, incycle,
outcycle );
break;
#endif
case TSP_COALESCED:
/* does not create a weight matrix, but sets weight in the adj lists */
convert2_to_tsp ( condnode1->genome, condnode2->genome,
condnode3->genome, adj_list, adj_pool,
num_cond, CIRCULAR );
score = coalestsp ( 2 * num_cond, condmedian->genome->genes, FALSE, /* cannot use median that does not exist */
condnode1->genome->genes,
condnode2->genome->genes,
condnode3->genome->genes, adj_list,
neighbors, stack, outcycle, degree,
otherEnd, edges, CIRCULAR );
break;
}
score += ( LARGENUM * num_genes ); /* I changed to num_genes from num_cond */
#ifdef DEBUG
fprintf ( outfile,
"for tree node #%3d, new median with score=%5d\n",
tree_node->tag, score );
for ( i = 0; i < num_genes; i++ )
{
fprintf ( outfile, "%3d, ", condmedian->genome->genes[i] );
}
fprintf ( outfile, "\n" );
fflush ( outfile );
#endif
tree_node->need_change = 0;
/* now use TSP score to compare to Hamming distance along the three
edges; for INV distance, compute it -- cannot mix the two!
if no improvement, restore the old label and exit */
switch ( distmethod )
{
case DIST_INV:
tmp_sc_parent =
bp_score ( condmedian, condnode1, num_cond, CIRCULAR,
distmethod, distmem, correction,
num_genes );
tmp_sc_lChild =
bp_score ( condmedian, condnode2, num_cond, CIRCULAR,
distmethod, distmem, correction,
num_genes );
tmp_sc_rChild =
bp_score ( condmedian, condnode3, num_cond, CIRCULAR,
distmethod, distmem, correction,
num_genes );
#ifdef DEBUG
fprintf ( outfile,
"new edge scores are %3d, %3d, and %3d\n",
tmp_sc_parent, tmp_sc_lChild, tmp_sc_rChild );
fprintf ( outfile,
"ptrs to old edge scores are %p, %p, and %p\n",
tree_node->sc_parent, tree_node->sc_lChild,
tree_node->sc_rChild );
fprintf ( outfile,
"old edge scores are %3d, %3d, and %3d\n",
*( tree_node->sc_parent ),
*( tree_node->sc_lChild ),
*( tree_node->sc_rChild ) );
fflush ( outfile );
#endif
delta =
( tmp_sc_parent + tmp_sc_lChild + tmp_sc_rChild ) -
( *( tree_node->sc_parent ) +
*( tree_node->sc_lChild ) +
*( tree_node->sc_rChild ) );
break;
case DIST_BP:
default:
delta = score - ( *( tree_node->sc_parent ) +
*( tree_node->sc_lChild ) +
*( tree_node->sc_rChild ) );
if ( delta < 0 )
{ /* get to same state as case DIST_INV */
tmp_sc_parent =
bp_score ( condmedian, condnode1, num_cond,
CIRCULAR, distmethod, distmem,
correction, num_genes );
tmp_sc_lChild =
bp_score ( condmedian, condnode2, num_cond,
CIRCULAR, distmethod, distmem,
correction, num_genes );
tmp_sc_rChild =
bp_score ( condmedian, condnode3, num_cond,
CIRCULAR, distmethod, distmem,
correction, num_genes );
#ifdef DEBUG
fprintf ( outfile,
"new edge scores are %3d, %3d, and %3d\n",
tmp_sc_parent, tmp_sc_lChild,
tmp_sc_rChild );
fflush ( outfile );
#endif
}
break;
}
#ifdef DEBUG
fprintf ( outfile, "score=%3d, delta=%3d\n", score, delta );
#endif
if ( delta < 0 )
{
/* accept the change */
if ( tree_node->lChild->tag < 0 )
tree_node->lChild->need_change = 1;
if ( tree_node->rChild->tag < 0 )
tree_node->rChild->need_change = 1;
if ( tree_node->parent->tag < 0 )
tree_node->parent->need_change = 1;
/* update the distances along the three edges (both ways) */
*( tree_node->sc_parent ) = tmp_sc_parent;
*( tree_node->sc_lChild ) = tmp_sc_lChild;
*( tree_node->sc_rChild ) = tmp_sc_rChild;
/* decode the median and assign it to the node */
decode3 ( tree_node->genome->genes, condmedian->genome->genes,
succ, decode, num_cond );
/* get ready for next loop */
*IMPROVED = TRUE;
#ifdef PRINT
*relabel += 1;
#endif
*best_so_far += delta;
}
else
{ /* restore old label */
for ( i = 0; i < num_genes; i++ )
{
tree_node->genome->genes[i] = genes[i];
}
}
} /* end condensation */
else
{ /* no condensation */
for ( i = 0; i < num_genes; i++ )
{ /* save old label */
genes[i] = tree_node->genome->genes[i];
}
/* which solver to call? */
/* force use of bbtsp if problem is too small */
realsolver = tspsolver;
if ( ( num_genes <= thresh ) && ( tspsolver != TSP_COALESCED ) )
realsolver = TSP_BBTSP;
switch ( realsolver )
{
case INVERSION_MEDIAN:
gen[0] = tree_node->parent->genome;
gen[1] = tree_node->lChild->genome;
gen[2] = tree_node->rChild->genome;
find_reversal_median ( tree_node->genome, gen, num_genes,
NULL );
/* find_inversion_median(tree_node->genome, gen, num_genes, distmem);*/
score = 0;
if ( CIRCULAR )
{
score += invdist_circular ( gen[0],
tree_node->genome,
num_genes, distmem );
score +=
invdist_circular ( gen[1], tree_node->genome,
num_genes, distmem );
score +=
invdist_circular ( gen[2], tree_node->genome,
num_genes, distmem );
}
else
{
score += invdist_noncircular ( gen[0],
tree_node->genome, 0,
num_genes, distmem );
score +=
invdist_noncircular ( gen[1], tree_node->genome,
0, num_genes, distmem );
score +=
invdist_noncircular ( gen[2], tree_node->genome,
0, num_genes, distmem );
}
break;
case INVERSION_MEDIAN_FAST:
gen[0] = tree_node->parent->genome;
gen[1] = tree_node->lChild->genome;
gen[2] = tree_node->rChild->genome;
score = 0;
if ( CIRCULAR )
{
albert_inversion_median_circular ( gen,
num_genes,
tree_node->genome->
genes );
score +=
invdist_circular ( gen[0], tree_node->genome,
num_genes, distmem );
score +=
invdist_circular ( gen[1], tree_node->genome,
num_genes, distmem );
score +=
invdist_circular ( gen[2], tree_node->genome,
num_genes, distmem );
}
else
{
albert_inversion_median_noncircular ( gen,
num_genes,
tree_node->
genome->genes );
score +=
invdist_noncircular ( gen[0], tree_node->genome,
0, num_genes, distmem );
score +=
invdist_noncircular ( gen[1], tree_node->genome,
0, num_genes, distmem );
score +=
invdist_noncircular ( gen[2], tree_node->genome,
0, num_genes, distmem );
}
break;
case TSP_BBTSP:
/* does not create a weight matrix, but sets weight in the adj lists */
convert2_to_tsp ( tree_node->parent->genome,
tree_node->lChild->genome,
tree_node->rChild->genome,
adj_list, adj_pool, num_genes,
CIRCULAR );
score =
bbtsp ( 2 * num_genes, tree_node->genome->genes,
use_median, tree_node->parent->genome->genes,
tree_node->lChild->genome->genes,
tree_node->rChild->genome->genes, adj_list,
neighbors, stack, outcycle, degree, otherEnd,
edges, CIRCULAR );
break;
#ifdef CONCORDE
case TSP_CHLINKERN:
/* creates a weight matrix -- more expensive! */
convert_to_tsp ( tree_node->parent->genome,
tree_node->lChild->genome,
tree_node->rChild->genome,
num_genes, CIRCULAR, weights );
score =
chlinkern ( 2 * num_genes, weights,
tree_node->genome->genes, incycle,
outcycle );
break;
case TSP_GREEDYLK:
/* creates a weight matrix -- more expensive! */
convert_to_tsp ( tree_node->parent->genome,
tree_node->lChild->genome,
tree_node->rChild->genome,
num_genes, CIRCULAR, weights );
score =
greedylk ( 2 * num_genes, weights,
tree_node->genome->genes, incycle,
outcycle );
break;
#endif
case TSP_COALESCED:
/* does not create a weight matrix, but sets weight in the adj lists */
convert2_to_tsp ( tree_node->parent->genome,
tree_node->lChild->genome,
tree_node->rChild->genome,
adj_list, adj_pool, num_genes,
CIRCULAR );
#ifdef DEBUG
fprintf ( outfile,
"in labeltree, about to call coalestsp\n" );
fflush ( outfile );
#endif
score =
coalestsp ( 2 * num_genes, tree_node->genome->genes,
use_median,
tree_node->parent->genome->genes,
tree_node->lChild->genome->genes,
tree_node->rChild->genome->genes,
adj_list, neighbors, stack, outcycle,
degree, otherEnd, edges, CIRCULAR );
break;
}
score += ( LARGENUM * num_genes );
#ifdef DEBUG
fprintf ( outfile,
"in labeltree, done with TSP, returned score is %3d\n",
score );
fflush ( outfile );
#endif
tree_node->need_change = 0;
/* now use TSP score to compare to Hamming distance along the three
edges; for INV distance, compute it -- cannot mix the two!
if no improvement, restore the old label and exit */
switch ( distmethod )
{
case DIST_INV:
/* avoid computing distances if the new label is the same as the
old one */
same = TRUE;
for ( i = 0; i < num_genes; i++ )
{
if ( genes[i] != tree_node->genome->genes[i] )
{
same = FALSE;
break;
}
}
if ( same )
goto done;
/* new label, so we have to compute distances */
tmp_sc_parent =
bp_score ( tree_node, tree_node->parent, num_genes,
CIRCULAR, distmethod, distmem, correction,
num_genes );
tmp_sc_lChild =
bp_score ( tree_node, tree_node->lChild, num_genes,
CIRCULAR, distmethod, distmem, correction,
num_genes );
tmp_sc_rChild =
bp_score ( tree_node, tree_node->rChild, num_genes,
CIRCULAR, distmethod, distmem, correction,
num_genes );
#ifdef DEBUG
fprintf ( outfile,
"new edge scores are %3d, %3d, and %3d\n",
tmp_sc_parent, tmp_sc_lChild, tmp_sc_rChild );
fprintf ( outfile,
"old edge scores are %3d, %3d, and %3d\n",
*( tree_node->sc_parent ),
*( tree_node->sc_lChild ),
*( tree_node->sc_rChild ) );
fflush ( outfile );
#endif
delta =
( tmp_sc_parent + tmp_sc_lChild + tmp_sc_rChild ) -
( *( tree_node->sc_parent ) +
*( tree_node->sc_lChild ) +
*( tree_node->sc_rChild ) );
#ifdef DEBUG
fprintf ( outfile,
"in labeltree, new (inv) edge scores are %3d, %3d, and %3d, delta is %3d\n",
tmp_sc_parent, tmp_sc_lChild, tmp_sc_rChild,
delta );
fflush ( outfile );
#endif
break;
case DIST_BP:
default:
delta = score - ( *( tree_node->sc_parent ) +
*( tree_node->sc_lChild ) +
*( tree_node->sc_rChild ) );
if ( delta < 0 )
{ /* get to same state as case DIST_INV */
tmp_sc_parent =
bp_score ( tree_node, tree_node->parent,
num_genes, CIRCULAR, distmethod,
distmem, correction, num_genes );
tmp_sc_lChild =
bp_score ( tree_node, tree_node->lChild,
num_genes, CIRCULAR, distmethod,
distmem, correction, num_genes );
tmp_sc_rChild =
bp_score ( tree_node, tree_node->rChild,
num_genes, CIRCULAR, distmethod,
distmem, correction, num_genes );
#ifdef DEBUG
fprintf ( outfile,
"new edge scores are %3d, %3d, and %3d\n",
tmp_sc_parent, tmp_sc_lChild,
tmp_sc_rChild );
fprintf ( outfile,
"old edge scores are %3d, %3d, and %3d\n",
*( tree_node->sc_parent ),
*( tree_node->sc_lChild ),
*( tree_node->sc_rChild ) );
fflush ( outfile );
#endif
}
break;
}
#ifdef DEBUG
fprintf ( outfile, "score=%3d, delta=%3d\n", score, delta );
#endif
if ( delta < 0 )
{
/* accept the change */
if ( tree_node->lChild->tag < 0 )
tree_node->lChild->need_change = 1;
if ( tree_node->rChild->tag < 0 )
tree_node->rChild->need_change = 1;
if ( tree_node->parent->tag < 0 )
tree_node->parent->need_change = 1;
/* update the distances along the three edges (both ways) */
*( tree_node->sc_parent ) = tmp_sc_parent;
*( tree_node->sc_lChild ) = tmp_sc_lChild;
*( tree_node->sc_rChild ) = tmp_sc_rChild;
/* get ready for next loop */
*IMPROVED = TRUE;
( *relabel )++;
*best_so_far += delta;
}
else
{ /* restore old label */
for ( i = 0; i < num_genes; i++ )
{
tree_node->genome->genes[i] = genes[i];
}
}
} /* end -- no condensation */
done:
tree_node->leaf = TRUE;
} /* end processing internal node */
#ifdef PREORDER
if ( !tree_node->lChild->leaf )
{
dfs_label_tree ( COND, root, tree_node->lChild, best_so_far, IMPROVED,
num_genes, num_genomes, weights, relabel, tspsolver,
thresh, adj_list, adj_pool, neighbors, stack,
incycle, outcycle, degree, otherEnd, edges, tpool,
labels, pred, succ, code, decode, condmedian,
condnode1, condnode2, condnode3, genes, CIRCULAR,
distmethod, distmem );
}
if ( tree_node->rChild )
if ( !tree_node->rChild->leaf )
{
dfs_label_tree ( COND, root, tree_node->rChild, best_so_far,
IMPROVED, num_genes, num_genomes, weights,
relabel, tspsolver, thresh, adj_list, adj_pool,
neighbors, stack, incycle, outcycle, degree,
otherEnd, edges, tpool, labels, pred, succ, code,
decode, condmedian, condnode1, condnode2,
condnode3, genes, CIRCULAR, distmethod,
distmem );
}
#endif
return;
}
int
score_tree ( struct tNode *treeNode, int num_genes, int CIRCULAR,
int distmethod, distmem_t * distmem, int correction )
{
int score = 0;
if ( treeNode == NULL )
return 0;
if ( treeNode->lChild )
{
*( treeNode->lChild->sc_parent ) = *( treeNode->sc_lChild ) =
bp_score ( treeNode, treeNode->lChild, num_genes, CIRCULAR,
distmethod, distmem, correction, num_genes );
score += *( treeNode->sc_lChild ) +
score_tree ( treeNode->lChild, num_genes, CIRCULAR, distmethod,
distmem, correction );
}
if ( treeNode->rChild )
{
*( treeNode->rChild->sc_parent ) = *( treeNode->sc_rChild ) =
bp_score ( treeNode, treeNode->rChild, num_genes, CIRCULAR,
distmethod, distmem, correction, num_genes );
score += *( treeNode->sc_rChild ) +
score_tree ( treeNode->rChild, num_genes, CIRCULAR, distmethod,
distmem, correction );
}
return score;
}
int
bp_score ( struct tNode *node1, struct tNode *node2, int num_genes,
int CIRCULAR, int distmethod, distmem_t * distmem, int correction,
int oldngenes )
{
int dist;
if ( node1 == NULL || node2 == NULL )
return 0;
switch ( distmethod )
{
case DIST_BP:
dist = hamming_distance ( node1->genome, node2->genome, num_genes,
CIRCULAR, distmem->hammingArr );
break;
case DIST_INV:
if ( correction )
{
if ( CIRCULAR )
dist =
ede ( invdist_circular
( node1->genome, node2->genome, num_genes,
distmem ), oldngenes );
else
dist =
ede ( invdist_noncircular
( node1->genome, node2->genome, 0, num_genes,
distmem ), oldngenes );
}
else
{
if ( CIRCULAR )
dist =
invdist_circular ( node1->genome, node2->genome,
num_genes, distmem );
else
dist =
invdist_noncircular ( node1->genome, node2->genome, 0,
num_genes, distmem );
}
break;
default:
dist = -1;
fprintf ( stderr, "ERROR: Bad distance method in bp_score()\n" );
}
return ( dist );
}
/* Use genome_list to initialize genome pointers in the leaves of the
tree.
*/
void
add_genomes_to_tree ( struct tNode *treeNode, struct genome_struct *labels,
struct genome_struct *genome_list, int num_genes )
{
int i, id;
struct genome_struct *gen;
if ( treeNode == NULL )
return;
if ( treeNode->leaf == TRUE )
{
/* because this is a leaf, the treeNode->tag is non-negative */
/* no need for malloc: just index into the labels array */
id = treeNode->tag;
gen = treeNode->genome = &labels[id];
gen->genome_num = id; /* not really redundant -- flags it as leaf */
id--;
for ( i = 0; i < num_genes; i++ )
{
gen->genes[i] = genome_list[id].genes[i];
}
gen->gnamePtr = genome_list[id].gnamePtr;
}
add_genomes_to_tree ( treeNode->lChild, labels, genome_list, num_genes );
add_genomes_to_tree ( treeNode->rChild, labels, genome_list, num_genes );
return;
}
void
restore_genome ( )
{
}
void
label_node ( struct tNode *tree_node, struct tNode *new_node, int num_genes )
{
}
void
leaf_tree ( struct tNode *tree )
{
if ( tree == NULL )
return;
if ( tree->tag < 0 )
tree->leaf = FALSE;
leaf_tree ( tree->lChild );
leaf_tree ( tree->rChild );
return;
}
void
init_change_bits ( struct tNode *tree )
{
if ( tree == NULL )
return;
if ( tree->tag < 0 )
{ /* internal node */
tree->need_change = 1;
}
else
{ /* leaf: labels are permanent */
tree->need_change = 0;
}
init_change_bits ( tree->lChild );
init_change_bits ( tree->rChild );
return;
}
/* find median for three node, node[0-2] and cNode is the store for median*/
void
findMedian ( struct tNode *node[3], struct tNode *cNode,
int *best_so_far, int num_genes,
int tspsolver, int thresh,
struct adj_struct *adj_list, struct adj_struct *adj_pool,
intpair_t * neighbors, int *stack, int *outcycle,
int *degree, int *otherEnd, edge_t * edges,
int *genes, int CIRCULAR,
int distmethod, distmem_t * distmem, int correction )
{
int score = 0, delta;
int i;
int realsolver, same, use_median = TRUE;
struct genome_struct *gen[3];
int tmp_sc_parent = 0, tmp_sc_lChild = 0, tmp_sc_rChild = 0;
for ( i = 0; i < num_genes; i++ )
{ /* save old label */
genes[i] = cNode->genome->genes[i];
}
/* which solver to call? */
/* force use of bbtsp if problem is too small */
realsolver = tspsolver;
if ( ( num_genes <= thresh ) && ( tspsolver != TSP_COALESCED ) )
realsolver = TSP_BBTSP;
switch ( realsolver )
{
case INVERSION_MEDIAN:
gen[0] = node[0]->genome;
gen[1] = node[1]->genome;
gen[2] = node[2]->genome;
find_reversal_median ( cNode->genome, gen, num_genes, NULL );
/* find_inversion_median(cNode->genome, gen, num_genes, distmem);*/
score = 0;
if ( CIRCULAR )
{
score += invdist_circular ( gen[0],
cNode->genome, num_genes,
distmem );
score +=
invdist_circular ( gen[1], cNode->genome, num_genes,
distmem );
score +=
invdist_circular ( gen[2], cNode->genome, num_genes,
distmem );
}
else
{
score += invdist_noncircular ( gen[0],
cNode->genome, 0, num_genes,
distmem );
score +=
invdist_noncircular ( gen[1], cNode->genome, 0, num_genes,
distmem );
score +=
invdist_noncircular ( gen[2], cNode->genome, 0, num_genes,
distmem );
}
break;
case INVERSION_MEDIAN_FAST:
gen[0] = node[0]->genome;
gen[1] = node[1]->genome;
gen[2] = node[2]->genome;
score = 0;
if ( CIRCULAR )
{
albert_inversion_median_circular ( gen,
num_genes,
cNode->genome->genes );
score +=
invdist_circular ( gen[0], cNode->genome, num_genes,
distmem );
score +=
invdist_circular ( gen[1], cNode->genome, num_genes,
distmem );
score +=
invdist_circular ( gen[2], cNode->genome, num_genes,
distmem );
}
else
{
albert_inversion_median_noncircular ( gen,
num_genes,
cNode->genome->genes );
score +=
invdist_noncircular ( gen[0], cNode->genome, 0, num_genes,
distmem );
score +=
invdist_noncircular ( gen[1], cNode->genome, 0, num_genes,
distmem );
score +=
invdist_noncircular ( gen[2], cNode->genome, 0, num_genes,
distmem );
}
break;
case TSP_BBTSP:
/* does not create a weight matrix, but sets weight in the adj lists */
convert2_to_tsp ( node[0]->genome, node[1]->genome,