/* Returns the median score of a potenial median with respect to three
specified "vertex" genomes. "gens" is assumed to be an array of at
least three pointers to genome_structs, and all genomes are assumed
to be of size "ngenes". Currently, a circular measure is always
used. */
int
median_score ( struct genome_struct **gens,
struct genome_struct *median, int ngenes, distmem_t * distmem )
{
return ( invdist_noncircular ( median, gens[0], 0, ngenes, distmem ) +
invdist_noncircular ( median, gens[1], 0, ngenes, distmem ) +
invdist_noncircular ( median, gens[2], 0, ngenes, distmem ) );
}
/* unichromosomal reversal distance, linear
Uses same parameter list as function of same name in GRAPPA
_v versions: graphstats return structure included
(used to be "verbose option is included")
*/
int invdist_circular(struct genome_struct *g1, struct genome_struct *g2,
int num_genes, distmem_t *distmem)
{
int offset;
offset = calculate_offset(g1, g2, num_genes);
return invdist_noncircular(g1, g2, offset, num_genes, distmem);
}
void calc_invmatrix(struct genome_struct *genomes, int num_genes, int num_genomes,
distmem_t *distmem, int CIRCULAR)
{
int i, j;
int dist;
for (i=0 ; i<num_genomes ; i++) {
for (j=i+1 ; j<num_genomes ; j++) {
if (CIRCULAR)
dist = invdist_circular(genomes+i, genomes+j, num_genes, distmem);
else
dist = invdist_noncircular(genomes+i, genomes+j, 0, num_genes, distmem);
}
}
return (void) dist;
}
int invdist_noncircular_nomem(struct genome_struct *g1,
struct genome_struct *g2,
int offset, int num_genes)
{
distmem_t distmem;
int dist;
mcdist_allocmem(num_genes,
0, /* num_chromosomes */
&distmem);
dist = invdist_noncircular(g1, g2, offset, num_genes, &distmem);
mcdist_freemem(&distmem);
return (dist);
}
int uhc_dist(
struct uhc_mem *uhcmem,
int i1,
int i2,
int num_genes,
int num_chromosomes,
int circular)
{
int d;
struct genome_struct *g1, *g2;
/* some of the distance routines modify the gene data, so we must
* work on copies
*/
if (num_chromosomes == 0) {
/* unichromosomal does not modify the input genomes */
g1 = &uhcmem->genome_list[i1];
g2 = &uhcmem->genome_list[i2];
} else {
/* multichromosomal does modify the genomes */
g1 = uhcmem->g1;
g2 = uhcmem->g2;
copy_genes(uhcmem->genome_list[i1].genes, g1->genes, num_genes);
copy_genes(uhcmem->genome_list[i2].genes, g2->genes, num_genes);
}
if (num_chromosomes == 0) {
if (circular) {
/* unichromosomal circular */
d = invdist_circular(g1, g2, num_genes, uhcmem->distmem);
} else {
/* unichromosomal linear */
d = invdist_noncircular(g1, g2, 0, num_genes, uhcmem->distmem);
}
} else {
/* multichromosomal */
d = mcdist_noncircular(g1, g2,
num_genes, num_chromosomes,
uhcmem->distmem,
(graphstats_t *) NULL);
}
return d;
}
void setinvmatrix(int **distmatrix,struct genome_struct *genomes,
int num_genes,int num_genomes,distmem_t *distmem,
int CIRCULAR)
{
int i, j;
for (i=0 ; i<num_genomes ; i++) {
distmatrix[i][i] = 0;
for (j=i+1 ; j<num_genomes ; j++) {
if (CIRCULAR)
distmatrix[i][j] = distmatrix[j][i] =
invdist_circular(genomes+i,genomes+j,num_genes,distmem);
else
distmatrix[i][j] = distmatrix[j][i] =
invdist_noncircular(genomes+i,genomes+j,0,num_genes,distmem);
}
}
return;
}
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;
}
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_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;
}
int
neighborj_score ( 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,
char *treeString )
{
int i, j;
int score;
double **D;
int *valid;
char **branch;
int maxConstSize;
int count;
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" );
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 ( genome_list + i,
genome_list + j, num_genes,
distmem );
else
D[i][j] =
( double ) invdist_noncircular ( genome_list + i,
genome_list + j, 0,
num_genes, distmem );
}
}
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 );
}
score = INT_INF;
count = 0;
neighborj_SK_trees ( 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,
num_genomes, D, valid, branch, maxConstSize,
&score, &count,
const_env, genes,
condense_succ, condense_decode,
orig_num_genes, correction, treeString );
#ifdef MPBPA
if ( MYPROC == 0 )
{
#endif
fprintf ( outfile,
"Number of neighbor-joining trees evaluated: %12d\n\n",
count );
fflush ( outfile );
#ifdef MPBPA
}
#endif
for ( i = 0; i < num_genomes; i++ )
free ( branch[i] );
free ( branch );
free ( valid );
for ( i = 0; i < num_genomes; i++ )
free ( D[i] );
free ( D );
return ( score );
}
void do_fn_external(int num_genes, int num_chromosomes, int num_genomes,
int circular,
int unsigned_dist,
int verbose,
struct genome_struct *genome_list,
char *ext_args)
{
int i, j;
int **distmatrix;
/* int dist_error; */
distmem_t *distmem;
int aborted=0;
//fprintf(outfile,"\nExternal function %s\n", ext_args);
if (verbose && !unsigned_dist) {
/*
do_fn_distmatrix_v(num_genes, num_chromosomes, num_genomes,
circular, unsigned_dist,
genome_list);
*/
//fprintf(outfile,"verbose, signed distance. Code deleted.\n");
return;
}
//fprintf(outfile,"\nDistance Matrix:\n");
/* allocate space for matrix */
distmatrix = (int **) e_malloc((num_genomes)*sizeof(int *), "distmatrix");
for (i=0; i < num_genomes; i++) {
distmatrix[i] = (int *) e_malloc((num_genomes)*sizeof(int), "distmatrix");
}
/* allocate memory for distance computations */
distmem = (distmem_t *) e_malloc(sizeof(distmem_t), "distmem");
mcdist_allocmem(num_genes,num_chromosomes,distmem);
/* compute the appropriate matrix */
if (unsigned_dist) {
//fprintf(outfile,"Unsigned distance. Code deleted.\n");
aborted++;
#if 0
set_unsigneddist_matrix(distmatrix, genome_list,
num_genes, num_chromosomes, num_genomes,
circular,
distmem,
&dist_error);
if (dist_error) {
//fprintf(outfile,"WARNING: These unsigned permutations are too complex;\n");
//fprintf(outfile,"some answers are approximated.\n");
}
#endif /* 0 */
} else if (num_chromosomes == 0) {
/* unichromosomal data */
#if 0
setinvmatrix(distmatrix,genome_list,
num_genes,num_genomes,
distmem,
/* circular already converted to equiv linear problem */
FALSE);
#endif /* 0 */
/* inline the code to demonstrate explicitly how distmem is used */
for (i=0 ; i<num_genomes ; i++) {
distmatrix[i][i] = 0;
for (j=i+1 ; j<num_genomes ; j++) {
if (circular)
distmatrix[i][j] = distmatrix[j][i] =
invdist_circular(genome_list+i,genome_list+j,
num_genes,distmem);
else
distmatrix[i][j] = distmatrix[j][i] =
invdist_noncircular(genome_list+i,genome_list+j,
0,num_genes,distmem);
}
}
} else {
#if 0
/* multichromosomal data */
setmcdistmatrix(distmatrix,genome_list,
num_genes,num_chromosomes,num_genomes,
distmem);
#endif /* 0 */
/* inline the code to demonstrate explicitly how distmem is used */
for (i=0 ; i<num_genomes ; i++) {
distmatrix[i][i] = 0;
for (j=i+1 ; j<num_genomes ; j++) {
distmatrix[i][j] = distmatrix[j][i] =
mcdist_noncircular(genome_list+i,genome_list+j,
num_genes,num_chromosomes,distmem,
(graphstats_t *)NULL); /* not verbose */
}
}
}
if (!aborted) {
/* display the matrix */
print_full_distmatrix(distmatrix,num_genomes,genome_list);
}
/* free the memory for distance computations */
mcdist_freemem(distmem); /* frees memory pointed to by fields of distmem */
free(distmem); /* frees the distmem structure itself */
/* free memory for the distance matrix */
for (i=num_genomes-1; i >=0 ; i--)
free(distmatrix[i]);
free(distmatrix);
}