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neighborj.c
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neighborj.c
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#include <stdio.h>
#include <stdlib.h>
#include "neighborj.h"
#include "invdist.h"
#include "const_tree.h"
#include "labeltree.h"
#include "inittree.h"
#include "specialinit.h"
#include "math.h"
#include "condense.h"
#define INT_INF MAX_RAND
#define DBL_INF (double)MAX_RAND
#define SMALLDELTA 0.001
double
neighborj_SN ( struct genome_struct *genomes, int num_genes, int num_genomes,
distmem_t * distmem, int CIRCULAR, int verbose )
{
int i, j, k;
double NJtreescore;
int num_clusters;
double **D;
int *valid;
double Dsum;
double Sij, minSij;
int mini, minj;
D = ( double ** ) malloc ( num_genomes * sizeof ( double * ) );
if ( D == ( double ** ) NULL )
fprintf ( stderr, "ERROR: D NULL\n" );
for ( i = 0; i < num_genomes; i++ )
{
D[i] = ( double * ) malloc ( num_genomes * sizeof ( double ) );
if ( D[i] == ( double * ) NULL )
fprintf ( stderr, "ERROR: D[i] NULL\n" );
}
valid = ( int * ) malloc ( num_genomes * sizeof ( int ) );
if ( valid == ( int * ) NULL )
fprintf ( stderr, "ERROR: valid NULL\n" );
NJtreescore = 0.0;
for ( i = 0; i < num_genomes; i++ )
valid[i] = TRUE;
Dsum = 0.0;
for ( i = 0; i < num_genomes; i++ )
{
for ( j = i + 1; j < num_genomes; j++ )
{
if ( CIRCULAR )
D[i][j] =
( double ) invdist_circular ( genomes + i, genomes + j,
num_genes, distmem );
else
D[i][j] =
( double ) invdist_noncircular ( genomes + i, genomes + j,
0, num_genes, distmem );
Dsum += D[i][j];
#ifdef DEBUG
fprintf ( outfile, "SN D[%3d][%3d]: %5.2f (Dsum: %5.2f)\n",
i, j, D[i][j], Dsum );
#endif
}
}
num_clusters = num_genomes;
while ( num_clusters > 2 )
{
minSij = DBL_INF;
mini = -1;
minj = -1;
for ( i = 0; i < num_genomes; i++ )
{
if ( valid[i] )
{
for ( j = i + 1; j < num_genomes; j++ )
{
if ( valid[j] )
{
Sij = 0.0;
for ( k = 0; k < num_genomes; k++ )
{
if ( ( k != i ) && ( k != j ) && valid[k] )
Sij +=
( i < k ? D[i][k] : D[k][i] ) + ( j <
k ?
D[j][k]
:
D[k]
[j] );
}
Sij /= 2.0 * ( ( double ) num_clusters - 2.0 );
Sij += 0.5 * D[i][j];
Sij +=
( 1.0 / ( ( double ) num_clusters - 2.0 ) ) *
( Dsum - D[i][j] );
#ifdef DEBUG
fprintf ( outfile, "SN S[%3d][%3d]: %5.2f\n", i, j,
Sij );
#endif
if ( Sij < minSij )
{
minSij = Sij;
mini = i;
minj = j;
}
}
}
}
}
if ( minSij == DBL_INF )
fprintf ( stderr, "ERROR: minSij Infinite\n" );
if ( ( mini == -1 ) || ( minj == -1 ) )
fprintf ( stderr, "ERROR: mini or minj not set\n" );
if ( ( valid[mini] == FALSE ) || ( valid[minj] == FALSE ) )
fprintf ( stderr, "ERROR: i or j cannot join\n" );
#ifdef VERYVERBOSE
if ( verbose )
{
fprintf ( outfile, "Saitou-Nei NJ:\t\t Step (%3d): ",
num_genomes - num_clusters + 1 );
fprintf ( outfile,
"Join %3d and %3d into %3d, edge weight= %5.2f\n", mini,
minj, mini, D[mini][minj] );
}
#endif
valid[minj] = FALSE;
for ( j = 0; j < mini; j++ )
{
if ( valid[j] )
{
if ( minj < j )
D[j][mini] = 0.5 * ( D[j][mini] + D[minj][j] );
else
D[j][mini] = 0.5 * ( D[j][mini] + D[j][minj] );
}
}
for ( j = mini + 1; j < num_genomes; j++ )
{
if ( valid[j] )
{
if ( minj < j )
D[mini][j] = 0.5 * ( D[mini][j] + D[minj][j] );
else
D[mini][j] = 0.5 * ( D[mini][j] + D[j][minj] );
}
}
NJtreescore += D[mini][minj];
Dsum -= D[mini][minj];
num_clusters--;
}
/* Must add last edge */
mini = minj = -1;
for ( i = 0; i < num_genomes; i++ )
if ( valid[i] )
{
if ( mini < 0 )
mini = i;
else
minj = i;
}
if ( ( mini < 0 ) || ( minj < 0 ) || ( mini >= minj ) )
fprintf ( stderr, "ERROR: cannot join last two neighbors\n" );
#ifdef VERYVERBOSE
if ( verbose )
{
fprintf ( outfile, "Saitou-Nei NJ:\t\t Step (%3d): ",
num_genomes - num_clusters + 1 );
fprintf ( outfile, "Join %3d and %3d into %3d, edge weight= %5.2f\n",
mini, minj, mini, D[mini][minj] );
}
#endif
NJtreescore += D[mini][minj];
if ( verbose )
{
fprintf ( outfile, "Saitou-Nei NJ\t\t Tree Score: %5.2f\n\n",
NJtreescore );
fflush ( outfile );
}
free ( valid );
for ( i = 0; i < num_genomes; i++ )
free ( D[i] );
free ( D );
return NJtreescore;
}
double
neighborj_SK ( struct genome_struct *genomes, int num_genes, int num_genomes,
distmem_t * distmem, int CIRCULAR, int verbose )
{
int i, j;
double NJtreescore;
int num_clusters;
double **D, Dij;
double *r;
int *valid;
double Sij, minSij;
int mini, minj;
D = ( double ** ) malloc ( num_genomes * sizeof ( double * ) );
if ( D == ( double ** ) NULL )
fprintf ( stderr, "ERROR: D NULL\n" );
for ( i = 0; i < num_genomes; i++ )
{
D[i] = ( double * ) malloc ( num_genomes * sizeof ( double ) );
if ( D[i] == ( double * ) NULL )
fprintf ( stderr, "ERROR: D[i] NULL\n" );
}
r = ( double * ) malloc ( num_genomes * sizeof ( double ) );
if ( r == ( double * ) NULL )
fprintf ( stderr, "ERROR: r NULL\n" );
valid = ( int * ) malloc ( num_genomes * sizeof ( int ) );
if ( valid == ( int * ) NULL )
fprintf ( stderr, "ERROR: valid NULL\n" );
NJtreescore = 0.0;
for ( i = 0; i < num_genomes; i++ )
valid[i] = TRUE;
for ( i = 0; i < num_genomes; i++ )
{
for ( j = i + 1; j < num_genomes; j++ )
{
if ( CIRCULAR )
D[i][j] =
( double ) invdist_circular ( genomes + i, genomes + j,
num_genes, distmem );
else
D[i][j] =
( double ) invdist_noncircular ( genomes + i, genomes + j,
0, num_genes, distmem );
}
}
num_clusters = num_genomes;
while ( num_clusters > 2 )
{
for ( i = 0; i < num_genomes; i++ )
{
if ( valid[i] )
{
r[i] = 0.0;
for ( j = 0; j < num_genomes; j++ )
if ( ( valid[j] ) && ( i != j ) )
{
if ( i < j )
r[i] += D[i][j];
else
r[i] += D[j][i];
}
r[i] /= ( ( double ) num_clusters - 2.0 );
}
}
minSij = DBL_INF;
mini = -1;
minj = -1;
for ( i = 0; i < num_genomes; i++ )
{
if ( valid[i] )
{
for ( j = i + 1; j < num_genomes; j++ )
{
if ( valid[j] )
{
Sij = D[i][j] - ( r[i] + r[j] );
#ifdef DEBUG
fprintf ( outfile, "S[%3d][%3d]: %5.2f\n", i, j,
Sij );
#endif
if ( Sij < minSij )
{
minSij = Sij;
mini = i;
minj = j;
}
}
}
}
}
if ( minSij == DBL_INF )
fprintf ( stderr, "ERROR: minSij Infinite\n" );
if ( ( mini == -1 ) || ( minj == -1 ) )
fprintf ( stderr, "ERROR: mini or minj not set\n" );
if ( ( valid[mini] == FALSE ) || ( valid[minj] == FALSE ) )
fprintf ( stderr, "ERROR: i or j cannot join\n" );
#ifdef VERYVERBOSE
if ( verbose )
{
fprintf ( outfile, "Studier-Keppler NJ:\t Step (%3d): ",
num_genomes - num_clusters + 1 );
fprintf ( outfile,
"Join %3d and %3d into %3d, edge weight= %5.2f\n", mini,
minj, mini, D[mini][minj] );
}
#endif
valid[minj] = FALSE;
Dij = D[mini][minj];
for ( j = 0; j < mini; j++ )
{
if ( valid[j] )
{
if ( minj < j )
D[j][mini] = 0.5 * ( D[j][mini] + D[minj][j] - Dij );
else
D[j][mini] = 0.5 * ( D[j][mini] + D[j][minj] - Dij );
}
}
for ( j = mini + 1; j < num_genomes; j++ )
{
if ( valid[j] )
{
if ( minj < j )
D[mini][j] = 0.5 * ( D[mini][j] + D[minj][j] - Dij );
else
D[mini][j] = 0.5 * ( D[mini][j] + D[j][minj] - Dij );
}
}
NJtreescore += Dij;
num_clusters--;
}
/* Must add last edge */
mini = minj = -1;
for ( i = 0; i < num_genomes; i++ )
if ( valid[i] )
{
if ( mini < 0 )
mini = i;
else
minj = i;
}
if ( ( mini < 0 ) || ( minj < 0 ) || ( mini >= minj ) )
fprintf ( stderr, "ERROR: cannot join last two neighbors\n" );
#ifdef VERYVERBOSE
if ( verbose )
{
fprintf ( outfile, "Studier-Keppler NJ:\t Step (%3d): ",
num_genomes - num_clusters + 1 );
fprintf ( outfile, "Join %3d and %3d into %3d, edge weight= %5.2f\n",
mini, minj, mini, D[mini][minj] );
}
#endif
NJtreescore += D[mini][minj];
if ( verbose )
{
fprintf ( outfile, "Studier-Keppler NJ\t Tree Score: %5.2f\n\n",
NJtreescore );
fflush ( outfile );
}
free ( valid );
free ( r );
for ( i = 0; i < num_genomes; i++ )
free ( D[i] );
free ( D );
return NJtreescore;
}
double
neighborj_SK_tree ( struct genome_struct *genomes,
int num_genes, int num_genomes,
distmem_t * distmem, int CIRCULAR, char *constTree )
{
int i, j;
double NJtreescore;
int num_clusters;
double **D, Dij;
double *r;
int *valid;
double Sij, minSij;
int mini, minj;
char **branch;
char *tmpbranch;
int maxConstSize;
D = ( double ** ) malloc ( num_genomes * sizeof ( double * ) );
if ( D == ( double ** ) NULL )
fprintf ( stderr, "ERROR: D NULL\n" );
for ( i = 0; i < num_genomes; i++ )
{
D[i] = ( double * ) malloc ( num_genomes * sizeof ( double ) );
if ( D[i] == ( double * ) NULL )
fprintf ( stderr, "ERROR: D[i] NULL\n" );
}
r = ( double * ) malloc ( num_genomes * sizeof ( double ) );
if ( r == ( double * ) NULL )
fprintf ( stderr, "ERROR: r NULL\n" );
valid = ( int * ) malloc ( num_genomes * sizeof ( int ) );
if ( valid == ( int * ) NULL )
fprintf ( stderr, "ERROR: valid NULL\n" );
branch = ( char ** ) malloc ( num_genomes * sizeof ( char * ) );
if ( branch == ( char ** ) NULL )
fprintf ( stderr, "ERROR: branch NULL\n" );
maxConstSize =
( ( int ) ceil ( log10 ( ( double ) num_genomes ) ) +
4 ) * num_genomes + 1;
for ( i = 0; i < num_genomes; i++ )
{
branch[i] = ( char * ) malloc ( maxConstSize * sizeof ( char ) );
if ( branch[i] == ( char * ) NULL )
fprintf ( stderr, "ERROR: branch[i] NULL\n" );
sprintf ( branch[i], "%d", i + 1 );
}
tmpbranch = ( char * ) malloc ( maxConstSize * sizeof ( char ) );
if ( tmpbranch == ( char * ) NULL )
fprintf ( stderr, "ERROR: tmpbranch NULL\n" );
NJtreescore = 0;
for ( i = 0; i < num_genomes; i++ )
valid[i] = TRUE;
for ( i = 0; i < num_genomes; i++ )
{
for ( j = i + 1; j < num_genomes; j++ )
{
if ( CIRCULAR )
D[i][j] =
( double ) invdist_circular ( genomes + i, genomes + j,
num_genes, distmem );
else
D[i][j] =
( double ) invdist_noncircular ( genomes + i, genomes + j,
0, num_genes, distmem );
}
}
num_clusters = num_genomes;
while ( num_clusters > 2 )
{
for ( i = 0; i < num_genomes; i++ )
{
if ( valid[i] )
{
r[i] = 0.0;
for ( j = 0; j < num_genomes; j++ )
if ( ( valid[j] ) && ( i != j ) )
{
if ( i < j )
r[i] += D[i][j];
else
r[i] += D[j][i];
}
r[i] /= ( ( double ) num_clusters - 2.0 );
}
}
minSij = DBL_INF;
mini = -1;
minj = -1;
for ( i = 0; i < num_genomes; i++ )
{
if ( valid[i] )
{
for ( j = i + 1; j < num_genomes; j++ )
{
if ( valid[j] )
{
Sij = D[i][j] - ( r[i] + r[j] );
#ifdef DEBUG
fprintf ( outfile, "S[%3d][%3d]: %5.2f\n", i, j,
Sij );
#endif
if ( Sij < minSij )
{
minSij = Sij;
mini = i;
minj = j;
}
}
}
}
}
if ( minSij == DBL_INF )
fprintf ( stderr, "ERROR: minSij Infinite\n" );
if ( ( mini == -1 ) || ( minj == -1 ) )
fprintf ( stderr, "ERROR: mini or minj not set\n" );
if ( ( valid[mini] == FALSE ) || ( valid[minj] == FALSE ) )
fprintf ( stderr, "ERROR: i or j cannot join\n" );
strcpy ( tmpbranch, branch[mini] );
sprintf ( branch[mini], "(%s,%s)", tmpbranch, branch[minj] );
valid[minj] = FALSE;
Dij = D[mini][minj];
for ( j = 0; j < mini; j++ )
{
if ( valid[j] )
{
if ( minj < j )
D[j][mini] = 0.5 * ( D[j][mini] + D[minj][j] - Dij );
else
D[j][mini] = 0.5 * ( D[j][mini] + D[j][minj] - Dij );
}
}
for ( j = mini + 1; j < num_genomes; j++ )
{
if ( valid[j] )
{
if ( minj < j )
D[mini][j] = 0.5 * ( D[mini][j] + D[minj][j] - Dij );
else
D[mini][j] = 0.5 * ( D[mini][j] + D[j][minj] - Dij );
}
}
NJtreescore += Dij;
num_clusters--;
}
/* Must add last edge */
mini = minj = -1;
for ( i = 0; i < num_genomes; i++ )
if ( valid[i] )
{
if ( mini < 0 )
mini = i;
else
minj = i;
}
if ( ( mini < 0 ) || ( minj < 0 ) || ( mini >= minj ) )
fprintf ( stderr, "ERROR: cannot join last two neighbors\n" );
NJtreescore += D[mini][minj];
sprintf ( constTree, "(%s,%s)", branch[mini], branch[minj] );
free ( tmpbranch );
for ( i = 0; i < num_genomes; i++ )
free ( branch[i] );
free ( branch );
free ( valid );
free ( r );
for ( i = 0; i < num_genomes; i++ )
free ( D[i] );
free ( D );
return NJtreescore;
}
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 );
}
int
neighborj_score_one ( 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, env_t * const_env,
int *genes, int *condense_succ, int *condense_decode,
int orig_num_genes, int correction )
{
double invscore_d;
int score;
char *constTree;
int maxConstSize;
int best_so_far;
char *treeString = NULL;
maxConstSize =
( ( int ) ceil ( log10 ( ( double ) num_genomes ) ) +
4 ) * num_genomes + 1;
constTree = ( char * ) malloc ( maxConstSize * sizeof ( char ) );
if ( constTree == ( char * ) NULL )
fprintf ( stderr, "ERROR: constTree NULL\n" );
invscore_d =
neighborj_SK_tree ( genome_list, num_genes, num_genomes, distmem,
CIRCULAR, constTree );
best_so_far = INT_INF;
score = neighborj_score_string ( constTree,
genome_list, num_genes, num_genomes,
distmem, CIRCULAR, tpool, edgepool,
labels, initmethod, COND, qpool,
adj_list, adj_pool, stack, degree,
otherEnd, neighbors, smalledges, edges,
outcycle,
pred1, pred2, picked, decode,
inittspsolver, triple, incycle,
tspsolver, distmethod, thresh, weights,
status, &best_so_far, const_env, genes,
condense_succ, condense_decode,
orig_num_genes, correction, treeString );
free ( constTree );
return ( score );
}
void
neighborj_SK_trees ( 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 num_clusters, double **orig_D, int *orig_valid,
char **orig_branch, int maxConstSize,
int *best_so_far, int *count,
env_t * const_env,
int *genes,
int *condense_succ, int *condense_decode,
int orig_num_genes, int correction, char *treeString )
{
int i, j, k, m;
double **D, Dij;
double *r;
int *valid;
double Sij, minSij;
int mini, minj;
char **branch;
char *tmpbranch;
int score;
char *constTree;
#ifdef DEBUG
fprintf ( outfile,
"neighborj_SK_trees(): best_so_far: %12d num_clust: %3d\n",
*best_so_far, num_clusters );
fflush ( outfile );
#endif
if ( num_clusters < 2 )
{
fprintf ( stderr, "ERROR: num_clusters < 2\n" );
exit ( -1 );
}
if ( num_clusters == 2 )
{
constTree = ( char * ) malloc ( maxConstSize * sizeof ( char ) );
if ( constTree == ( char * ) NULL )
fprintf ( stderr, "ERROR: constTree NULL\n" );
/* Must add last edge */
mini = minj = -1;
for ( i = 0; i < num_genomes; i++ )
if ( orig_valid[i] )
{
if ( mini < 0 )
mini = i;
else
minj = i;
}
if ( ( mini < 0 ) || ( minj < 0 ) || ( mini >= minj ) )
fprintf ( stderr, "ERROR: cannot join last two neighbors\n" );
sprintf ( constTree, "(%s,%s)", orig_branch[mini],
orig_branch[minj] );
score = neighborj_score_string ( constTree,
genome_list, num_genes, num_genomes,
distmem, CIRCULAR, tpool, edgepool,
labels, initmethod, COND, qpool,
adj_list, adj_pool, stack, degree,
otherEnd, neighbors, smalledges,
edges, outcycle, pred1, pred2,
picked, decode, inittspsolver,
triple, incycle, tspsolver,
distmethod, thresh, weights, status,
best_so_far, const_env, genes,
condense_succ, condense_decode,
orig_num_genes, correction,
treeString );
( *count )++;
free ( constTree );
return;
}
r = ( double * ) malloc ( num_genomes * sizeof ( double ) );
if ( r == ( double * ) NULL )
fprintf ( stderr, "ERROR: r NULL\n" );
valid = ( int * ) malloc ( num_genomes * sizeof ( int ) );
if ( valid == ( int * ) NULL )
fprintf ( stderr, "ERROR: valid NULL\n" );
for ( i = 0; i < num_genomes; i++ )
valid[i] = orig_valid[i];
branch = ( char ** ) malloc ( num_genomes * sizeof ( char * ) );
if ( branch == ( char ** ) NULL )
fprintf ( stderr, "ERROR: branch NULL\n" );
for ( i = 0; i < num_genomes; i++ )
{
branch[i] = ( char * ) malloc ( maxConstSize * sizeof ( char ) );
if ( branch[i] == ( char * ) NULL )
fprintf ( stderr, "ERROR: branch[i] NULL\n" );
strcpy ( branch[i], orig_branch[i] );
}
tmpbranch = ( char * ) malloc ( maxConstSize * sizeof ( char ) );
if ( tmpbranch == ( char * ) NULL )
fprintf ( stderr, "ERROR: tmpbranch NULL\n" );
D = ( double ** ) malloc ( num_genomes * sizeof ( double * ) );
if ( D == ( double ** ) NULL )
fprintf ( stderr, "ERROR: D NULL\n" );
for ( i = 0; i < num_genomes; i++ )
{
D[i] = ( double * ) malloc ( num_genomes * sizeof ( double ) );
if ( D[i] == ( double * ) NULL )
fprintf ( stderr, "ERROR: D[i] NULL\n" );
}
/* num_clusters > 2 */
for ( i = 0; i < num_genomes; i++ )
{
if ( valid[i] )
{
r[i] = 0.0;
for ( j = 0; j < num_genomes; j++ )
if ( ( valid[j] ) && ( i != j ) )
{
if ( i < j )
r[i] += orig_D[i][j];
else
r[i] += orig_D[j][i];
}
r[i] /= ( ( double ) num_clusters - 2.0 );
}
}
minSij = DBL_INF;
for ( i = 0; i < num_genomes; i++ )
{
if ( valid[i] )
{
for ( j = i + 1; j < num_genomes; j++ )
{
if ( valid[j] )
{
Sij = orig_D[i][j] - ( r[i] + r[j] );
#ifdef DEBUG
fprintf ( outfile, "S[%3d][%3d]: %5.2f\n", i, j, Sij );
#endif
if ( Sij < minSij )
{
minSij = Sij;
}
}
}
}
}
if ( minSij == DBL_INF )
fprintf ( stderr, "ERROR: minSij Infinite\n" );
for ( i = 0; i < num_genomes; i++ )
{
if ( valid[i] )
{
for ( j = i + 1; j < num_genomes; j++ )
{
if ( valid[j] )
{
if ( fabs ( minSij - ( orig_D[i][j] - ( r[i] + r[j] ) ) )