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invdist.c
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#include <stdio.h>
#include <stdlib.h>
#include "invdist.h"
#include "structs.h"
#ifdef TESTING
double time_linear, time_BH;
#endif
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
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;
}
void
calc_invmatrix_BH ( 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_BH ( genomes + i, genomes + j, num_genes,
distmem );
else
dist =
invdist_noncircular_BH ( genomes + i, genomes + j, 0,
num_genes, distmem );
}
}
return;
}
int
calculate_offset ( struct genome_struct *g1, struct genome_struct *g2,
int num_genes )
{
int i;
int gA;
int *genes2;
#ifdef DEBUG
for ( i = 0; i < num_genes; i++ )
{
fprintf ( outfile, "calc_offset: g1[%3d]: %3d g2[%3d]: %3d\n",
i, g1->genes[i], i, g2->genes[i] );
}
#endif
genes2 = g2->genes;
gA = g1->genes[0];
for ( i = 0; i < num_genes; i++ )
{
if ( genes2[i] == gA )
return ( i );
if ( genes2[i] == -gA )
return ( i + num_genes );
}
fprintf ( stderr, "ERROR: calc_offset() could not locate gene %d\n", gA );
return ( -1 );
}
int
num_breakpoints ( int *perm, int size )
{
int i, b;
int pA, pA1;
int pB, pB1;
b = 0;
if ( perm[1] != 1 )
b++;
for ( i = 2; i < size - 1; i += 2 )
{
pA = perm[i];
pA1 = ( pA == size ? 1 : pA + 1 );
pB = perm[i + 1];
pB1 = ( pB == size ? 1 : pB + 1 );
if ( ( pB != pA1 ) && ( pA != pB1 ) )
b++;
}
return ( b );
}
int
num_cycles ( int *perm, int size, distmem_t * distmem )
{
int *done;
int i, ind, j1, j2;
int next;
int c;
int *greyEdges;
int *invperm;
int *cycle;
done = distmem->done;
greyEdges = distmem->greyEdges;
invperm = distmem->done;
cycle = distmem->labeled;
c = 0;
#if 0
/* This is now implicit */
/* set black -edges */
for ( i = 0; i < size; i += 2 )
{
blackEdges[i] = i + 1;
blackEdges[i + 1] = i;
}
#endif
/* set grey -edges */
for ( i = 0; i < size; i++ )
{
invperm[perm[i]] = i;
greyEdges[i] = -1;
}
j1 = invperm[1];
if ( j1 != 1 )
greyEdges[0] = j1;
for ( i = 1; i < size - 1; i += 2 )
{
ind = perm[i];
if ( ind < perm[i + 1] )
{
j1 = invperm[ind - 1];
j2 = invperm[ind + 2];
}
else
{
j1 = invperm[ind + 1];
j2 = invperm[ind - 2];
}
if ( j1 != i - 1 )
{
greyEdges[i] = j1;
}
if ( j2 != i + 2 )
{
greyEdges[i + 1] = j2;
}
}
j1 = invperm[size - 2];
if ( j1 != size - 2 )
greyEdges[size - 1] = j1;
#ifdef DEBUG
for ( i = 0; i < size; i++ )
{
fprintf ( stdout, "i: %3d Grey edge: (%3d, %3d)\n", perm[i],
perm[i], greyEdges[i] == -1 ? -1 : perm[greyEdges[i]] );
}
#endif
for ( i = 0; i < size; i++ )
done[i] = 0;
for ( i = 0; i < size; i++ )
{
if ( done[i] == 0 && greyEdges[i] != -1 )
{
cycle[i] = i;
done[i] = 1;
next = i;
do
{
if ( next % 2 == 0 )
next++;
else
next--;
done[next] = 1;
cycle[next] = i;
next = greyEdges[next];
done[next] = 1;
cycle[next] = i;
}
while ( next != i );
c++;
}
}
return ( c );
}
int
num_cycles_BH ( int *perm, int size, distmem_t * distmem )
{
int *done;
int i, ind, j1, j2;
int next;
int c;
int *greyEdges;
int *invperm;
done = distmem->done;
greyEdges = distmem->greyEdges;
invperm = distmem->done;
c = 0;
#if 0
/* This is now implicit */
/* set black -edges */
for ( i = 0; i < size; i += 2 )
{
blackEdges[i] = i + 1;
blackEdges[i + 1] = i;
}
#endif
/* set grey -edges */
for ( i = 0; i < size; i++ )
{
invperm[perm[i]] = i;
greyEdges[i] = -1;
}
j1 = invperm[1];
if ( j1 != 1 )
greyEdges[0] = j1;
for ( i = 1; i < size - 1; i += 2 )
{
ind = perm[i];
if ( ind < perm[i + 1] )
{
j1 = invperm[ind - 1];
j2 = invperm[ind + 2];
}
else
{
j1 = invperm[ind + 1];
j2 = invperm[ind - 2];
}
if ( j1 != i - 1 )
{
greyEdges[i] = j1;
}
if ( j2 != i + 2 )
{
greyEdges[i + 1] = j2;
}
}
j1 = invperm[size - 2];
if ( j1 != size - 2 )
greyEdges[size - 1] = j1;
#ifdef DEBUG
for ( i = 0; i < size; i++ )
{
fprintf ( stdout, "i: %3d Grey edge: (%3d, %3d)\n", perm[i],
perm[i], greyEdges[i] == -1 ? -1 : perm[greyEdges[i]] );
}
#endif
for ( i = 0; i < size; i++ )
done[i] = 0;
for ( i = 0; i < size; i++ )
{
if ( done[i] == 0 && greyEdges[i] != -1 )
{
done[i] = 1;
next = i;
do
{
if ( next % 2 == 0 )
next++;
else
next--;
done[next] = 1;
next = greyEdges[next];
done[next] = 1;
}
while ( next != i );
c++;
}
}
return ( c );
}
void
connected_component ( int size, distmem_t * distmem, int *num_components )
{
int i;
int stack_ptr;
int *greyEdges;
int *cycle, *range, *cc;
component_t *components;
int *stack_root, *stack_range;
int *parent, *next;
int right, p;
#ifdef TESTING
struct timeval tm;
double time0, time1;
#endif
#ifdef TESTING
gettimeofday ( &tm, NULL );
time0 = ( double ) tm.tv_sec + ( double ) tm.tv_usec / 1000000.0;
#endif
greyEdges = distmem->greyEdges;
next = stack_root = distmem->stack;
range = distmem->oriented;
stack_range = cc = distmem->cc;
parent = cycle = distmem->labeled;
components = distmem->components;
stack_ptr = -1;
*num_components = 0;
/* Use Linear algorithm to compute connected component */
for ( i = 0; i < size; i++ )
{
if ( greyEdges[i] == -1 )
continue;
range[cycle[i]] = i;
}
for ( i = 0; i < size; i++ )
{
if ( greyEdges[i] == -1 )
continue; /*it is self loop,discard it */
if ( parent[i] == i )
{
stack_ptr++;
stack_root[stack_ptr] = i;
stack_range[stack_ptr] = range[i];
}
else
{ /*check the top of stack for intersection */
right = i;
#ifdef DEBUG
fprintf ( stdout, "top:%d,rang:%d,i:%d,parent[i]:%d\n",
stack_root[stack_ptr], stack_range[stack_ptr], i,
parent[i] );
fflush ( stdout );
#endif
while ( stack_root[stack_ptr] > parent[i] )
{
/*union top to the i's connected component */
parent[stack_root[stack_ptr]] = parent[i];
if ( right < stack_range[stack_ptr] )
right = stack_range[stack_ptr]; /*extend the active range */
stack_ptr--;
}
if ( stack_range[stack_ptr] < right )
stack_range[stack_ptr] = right;
if ( stack_range[stack_ptr] <= i )
{
/*the top connected-component is INACTIVE */
components[*num_components].index = stack_root[stack_ptr];
( *num_components )++;
stack_ptr--;
}
}
}
/*turn the forest to set of linked lists whose list head is index of
component */
for ( i = 0; i < size; i++ )
next[i] = -1;
for ( i = 0; i < size; i++ )
{
if ( greyEdges[i] == -1 )
cc[i] = -1;
else if ( i != parent[i] )
{
/* insert i between parent(i) and next of parent(i) */
next[i] = next[parent[i]];
next[parent[i]] = i;
}
}
/*label each node with its root */
for ( i = 0; i < *num_components; i++ )
{
p = components[i].index;
while ( p != -1 )
{
cc[p] = i;
p = next[p];
}
}
#ifdef TESTING
gettimeofday ( &tm, NULL );
time1 = ( double ) tm.tv_sec + ( double ) tm.tv_usec / 1000000.0;
time_linear += time1 - time0;
#endif
return;
}
void
num_hurdles_and_fortress ( int *perm, int size,
int *num_hurdles, int *num_fortress,
distmem_t * distmem )
{
int cIdx;
int i, j;
int *oriented, *cc, *labeled;
component_t *components;
int num_components;
int num_oriented;
int first_comp, last_comp, num_block;
int num_superhurdles;
int *greyEdges;
/* By default, set number of hurdles and fortresses to 0 */
*num_hurdles = 0;
*num_fortress = 0;
greyEdges = distmem->greyEdges;
oriented = distmem->oriented;
cc = distmem->cc;
labeled = distmem->labeled;
components = distmem->components;
connected_component ( size, distmem, &num_components );
if ( num_components == 0 )
{
#ifdef DEBUG
fprintf ( stdout, "No components -- quick exit\n" );
#endif
return;
}
/* Calculate if each gray edge is oriented or unoriented */
/* At the same time, label the connected component of a vertex as the
index of its root */
for ( i = 0; i < size; i++ )
{
j = greyEdges[i];
if ( j == -1 )
{
oriented[i] = FALSE;
}
else
{
if ( i < j )
{
if ( ( j - i ) % 2 != 0 )
{
oriented[i] = FALSE;
oriented[j] = FALSE;
}
else
{
oriented[i] = TRUE;
oriented[j] = TRUE;
}
}
}
}
/* Look for any vertices that are "labeled".
These are the roots of the cnnected components.
Record them in the "components" array,
and set num_components.
*/
/* If a component contains an oriented vertex then it is oriented.
Otherwise, the component is unoriented. */
for ( i = 0; i < num_components; i++ )
{
components[i].oriented = FALSE;
}
for ( i = 0; i < size; i++ )
{
if ( oriented[i] == 1 )
components[cc[i]].oriented = TRUE;
}
/* Count nonoriented components */
num_oriented = 0;
for ( i = 0; i < num_components; i++ )
{
if ( components[i].oriented == FALSE )
{
num_oriented++;
}
}
if ( num_oriented == 0 )
{
#ifdef DEBUG
fprintf ( stdout, "Quick exit -- no hurdles\n" );
#endif
return;
}
for ( i = 0; i < num_components; i++ )
{
components[i].blocks = 0;
components[i].hurdle = 0;
components[i].left = -1;
components[i].right = -1;
}
/* HURDLES
Hurdles are a subset of the nonoriented components.
There are two types of hurdles (in the KST-sense):
"simple" and "superhurdle".
First, we implicitly eliminate oriented components.
Second, if a nonoriented component is one contiguous block of
vertices, it is a hurdle.
Third, if a hurdle "protects" the same non-hurdle on its left and
right side, then it is a "superhurdle".
*/
first_comp = -1;
last_comp = -1;
num_block = -1;
for ( i = 0; i < size; i++ )
{
cIdx = cc[i];
if ( cIdx != -1 )
{
if ( components[cIdx].oriented == FALSE )
{
if ( cIdx != last_comp )
{
if ( last_comp == -1 )
{
first_comp = cIdx;
}
else
{
components[last_comp].right = cIdx;
components[cIdx].left = last_comp;
}
last_comp = cIdx;
num_block++;
components[cIdx].blocks++;
}
}
}
}
#ifdef DEBUG
for ( i = 0; i < num_components; i++ )
{
if ( components[i].oriented == FALSE )
{
fprintf ( stdout, "nonoriented component %3d: blocks: %3d\n",
i, components[i].blocks );
}
}
#endif
for ( i = 0; i < num_components; i++ )
{
if ( ( components[i].oriented == FALSE )
&& ( components[i].blocks == 1 ) )
{
#ifdef DEBUG
fprintf ( stdout, "nonoriented component %3d: blocks: %3d\n",
i, components[i].blocks );
#endif
components[i].hurdle = HURDLE;
( *num_hurdles )++;
}
}
if ( ( first_comp == last_comp )
&& ( components[first_comp].blocks == 2 ) )
{
components[first_comp].hurdle = ( HURDLE | GREATHURDLE );
( *num_hurdles )++;
}
if ( *num_hurdles < 3 )
return;
num_superhurdles = 0;
for ( i = 0; i < num_components; i++ )
{
if ( components[i].hurdle )
{
if ( ( components[i].left == components[i].right ) &&
( components[i].left != -1 ) )
{
if ( ( components[components[i].left].blocks == 2 ) &&
( ( components[components[i].left].
hurdle & GREATHURDLE ) == 0 ) )
{
#ifdef DEBUG
fprintf ( stdout, "Component %3d is a superhurdle \n",
i );
#endif
components[i].hurdle |= SUPERHURDLE;
num_superhurdles++;
}
else
{
return;
}
}
else
{
return;
}
}
}
#ifdef DEBUG
fprintf ( stdout, "Number of superhurdles: %3d\n", num_superhurdles );
#endif
/* Set num_fortress if there are an odd number of hurdles,
all of which are superhurdles. */
if ( ( *num_hurdles == num_superhurdles )
&& ( num_superhurdles % 2 == 1 ) )
*num_fortress = 1;
return;
}
void
connected_component_BH ( int size, distmem_t * distmem, int *num_components )
{
UFelem *uf;
int *stack;
int stackPtr;
int cIdx;
int i, j, v;
int s, eB, eE;
int *oriented, *cc, *labeled;
component_t *components;
int *greyEdges;
#ifdef TESTING
struct timeval tm;
double time0, time1;
#endif
#ifdef TESTING
gettimeofday ( &tm, NULL );
time0 = ( double ) tm.tv_sec + ( double ) tm.tv_usec / 1000000.0;
#endif
greyEdges = distmem->greyEdges;
uf = distmem->uf;
UFcreate ( uf, size );
stack = distmem->stack;
oriented = distmem->oriented;
cc = distmem->cc;
labeled = distmem->labeled;
components = distmem->components;
stackPtr = 0;
/* Use Berman & Hannenhalli to label the connected components */
for ( i = 0; i < size; i++ )
{
/* if i is the beginning of an edge (i, j) */
j = greyEdges[i];
if ( j != -1 )
{
if ( i < j )
{
/* Create a new component with set (i,j) and handle (i,j) */
uf[i].B = i;
uf[i].E = j;
uf[i].handleB = i;
uf[i].handleE = j;
/* push i onto the stack */
stack[stackPtr++] = i;
}
else
{
/* if i is the end of an edge */
/* This always has to be the case in the else loop */
/* C <- Find(i) */
cIdx = UFfind ( uf, j );
/* s <- handle(C).B */
s = uf[cIdx].handleB;
/* While top >= s */
while ( ( stackPtr > 0 ) && ( stack[stackPtr - 1] >= s ) )
{
/* C <- Union(Find(pop), C) */
cIdx =
UFunion ( uf, UFfind ( uf, stack[stackPtr - 1] ),
cIdx );
stackPtr--;
}
/* e <- handle(C) */
eB = uf[cIdx].handleB;
eE = uf[cIdx].handleE;
/* if e.E > i */
if ( eE > i )
{ /* if C is active */
/* push(e.B) */
stack[stackPtr++] = eB;
}
}
}
}
#ifdef DEBUG
for ( i = 0; i < size; i++ )
{
j = greyEdges[i];
if ( j != -1 )
{
if ( i < j )
{
cIdx = UFfind ( uf, i );
fprintf ( stdout,
"Grey Edge (%3d, %3d): component: %3d handle (%3d,%3d)\n",
perm[i], perm[j],
cIdx,
perm[uf[cIdx].handleB], perm[uf[cIdx].handleE] );
}
}
}
#endif
/* Calculate if each gray edge is oriented or unoriented */
/* At the same time, label the connected component of a vertex as the
index of its root */
for ( i = 0; i < size; i++ )
labeled[i] = -1;
for ( i = 0; i < size; i++ )
{
j = greyEdges[i];
if ( j == -1 )
{
cc[i] = -1;
}
else
{
if ( i < j )
{
v = cc[i] = cc[j] = UFfind ( uf, i );
labeled[v] = 1;
}
}
}
/* Look for any vertices that are "labeled".
These are the roots of the cnnected components.
Record them in the "components" array,
and set num_components.
*/
*num_components = 0;
for ( i = 0; i < size; i++ )
{
if ( labeled[i] == 1 )
{
labeled[i] = *num_components;
( *num_components )++;
}
}
/* Set the component label of each vertex to the label of its
component root. */
for ( i = 0; i < size; i++ )
{
if ( cc[i] != -1 )
cc[i] = labeled[cc[i]];
}
#ifdef TESTING
gettimeofday ( &tm, NULL );
time1 = ( double ) tm.tv_sec + ( double ) tm.tv_usec / 1000000.0;
time_BH += time1 - time0;
#endif
return;
}
void
num_hurdles_and_fortress_BH ( int *perm, int size,
int *num_hurdles, int *num_fortress,
distmem_t * distmem )
{
int cIdx;
int i, j;
int *oriented, *cc;
component_t *components;
int num_components;
int num_oriented;
int first_comp, last_comp, num_block;
int num_superhurdles;
int *greyEdges;
/* By default, set number of hurdles and fortresses to 0 */
*num_hurdles = 0;
*num_fortress = 0;
greyEdges = distmem->greyEdges;
oriented = distmem->oriented;
cc = distmem->cc;
components = distmem->components;
connected_component_BH ( size, distmem, &num_components );
for ( i = 0; i < size; i++ )
{
j = greyEdges[i];
if ( j == -1 )
{
oriented[i] = FALSE;
}
else
{
if ( i < j )
{
if ( ( j - i ) % 2 != 0 )
{
oriented[i] = FALSE;
oriented[j] = FALSE;
}
else
{
oriented[i] = TRUE;
oriented[j] = TRUE;
}
}
}
}
/* Look for any vertices that are "labeled".
These are the roots of the cnnected components.
Record them in the "components" array,
and set num_components.
*/
if ( num_components == 0 )
{
#ifdef DEBUG
fprintf ( stdout, "No components -- quick exit\n" );
#endif
return;
}
/* If a component contains an oriented vertex then it is oriented.
Otherwise, the component is unoriented. */
for ( i = 0; i < num_components; i++ )
{
components[i].oriented = FALSE;
}
for ( i = 0; i < size; i++ )
{
if ( oriented[i] == 1 )
components[cc[i]].oriented = TRUE;
}
#ifdef DEBUG
for ( i = 0; i < num_components; i++ )
{
fprintf ( stdout,
"Component: %3d: index: %3d handle: (%3d, %3d) Oriented: %1d\n",
i, v = components[i].index,
perm[uf[v].handleB], perm[uf[v].handleE],
components[i].oriented );
}
#endif
/* Count nonoriented components */
num_oriented = 0;
for ( i = 0; i < num_components; i++ )
{
if ( components[i].oriented == FALSE )
{
num_oriented++;
}
}
if ( num_oriented == 0 )
{
#ifdef DEBUG
fprintf ( stdout, "Quick exit -- no hurdles\n" );
#endif
return;
}
for ( i = 0; i < num_components; i++ )
{
components[i].blocks = 0;
components[i].hurdle = 0;
components[i].left = -1;
components[i].right = -1;
}
/* HURDLES
Hurdles are a subset of the nonoriented components.
There are two types of hurdles (in the KST-sense):
"simple" and "superhurdle".
First, we implicitly eliminate oriented components.
Second, if a nonoriented component is one contiguous block of
vertices, it is a hurdle.
Third, if a hurdle "protects" the same non-hurdle on its left and
right side, then it is a "superhurdle".
*/
first_comp = -1;
last_comp = -1;
num_block = -1;
for ( i = 0; i < size; i++ )
{
cIdx = cc[i];
if ( cIdx != -1 )
{
if ( components[cIdx].oriented == FALSE )
{
if ( cIdx != last_comp )
{
if ( last_comp == -1 )
{
first_comp = cIdx;
}
else
{