int main()
{
int weights[MAX]; //input array of weights
int size; //size of array for class
int class; //input of class size
size = getweights(weights);
class = getclass(size);
sort(weights, size);
findmin(weights, size, class);
return(0);
}
/** gets index of the node in a given set of nodes with maximum weight */
static
int getMaxWeightIndex(
TCLIQUE_GETNNODES((*getnnodes)), /**< user function to get the number of nodes */
TCLIQUE_GETWEIGHTS((*getweights)), /**< user function to get the node weights */
TCLIQUE_GRAPH* tcliquegraph, /**< pointer to graph data structure */
int* V, /**< non-zero weighted nodes for branching */
int nV /**< number of non-zero weighted nodes for branching */
)
{
const TCLIQUE_WEIGHT* weights;
TCLIQUE_WEIGHT maxweight;
int maxweightindex;
int i;
assert(getnnodes != NULL);
assert(getweights != NULL);
assert(tcliquegraph != NULL);
assert(nV > 0);
weights = getweights(tcliquegraph);
maxweightindex = -1;
maxweight = 0;
/* try to improve maxweight */
for( i = 0 ; i < nV; i++ )
{
assert(0 <= V[i] && V[i] < getnnodes(tcliquegraph));
assert(weights[V[i]] > 0);
if( weights[V[i]] > maxweight)
{
/* node has larger weight */
maxweight = weights[V[i]];
maxweightindex = i;
}
}
assert(maxweightindex >= 0);
return maxweightindex;
}
int main(int argc, char **argv)
{
char **eglist ;
int numeg ;
int i, j, k, pos;
int *vv ;
SNP *cupt, *cupt2 ;
Indiv *indx ;
double y1, y2, y ;
int n0, n1, nkill ;
int nindiv = 0 ;
int nignore, numrisks = 1 ;
SNP **xsnplist ;
Indiv **xindlist ;
int *xindex ;
int nrows, ncols, m ;
double *XTX, *cc, *evecs, *ww ;
double *lambda ;
double *tvecs ;
int weightmode = NO ;
int t ;
double *xmean, *xfancy ;
double *ldmat = NULL, *ldmat2 = NULL;
double *ldvv = NULL, *ldvv2 = NULL, *vv2 = NULL ;
int chrom, numclear ;
double gdis ;
int outliter, numoutiter, *badlist, nbad ;
int a, b, n ;
FILE *outlfile ;
int xblock, blocksize=10000 ;
double *tblock ;
OUTLINFO *outpt ;
int *idperm, *vecind ; // for sort
readcommands(argc, argv) ;
printf("## smartrel version: %s\n", WVERSION) ;
packmode = YES ;
setomode(&outputmode, omode) ;
if (parname == NULL) return 0 ;
if (xchrom == (numchrom+1)) noxdata = NO ;
if (fstonly) {
printf("fstonly\n") ;
numeigs = 0 ;
numoutliter = 0 ;
numoutiter = 0 ;
outputname = NULL ;
snpeigname = NULL ;
}
if (fancynorm) printf("norm used\n\n") ;
else printf("no norm used\n\n") ;
nostatslim = MAX(nostatslim, 3) ;
outlfile = ofile = stdout;
if (outputname != NULL) openit(outputname, &ofile, "w") ;
if (outliername != NULL) openit(outliername, &outlfile, "w") ;
if (fstdetailsname != NULL) openit(fstdetailsname, &fstdetails, "w") ;
numsnps =
getsnps(snpname, &snpmarkers, 0.0, badsnpname, &nignore, numrisks) ;
numindivs = getindivs(indivname, &indivmarkers) ;
k = getgenos(genotypename, snpmarkers, indivmarkers,
numsnps, numindivs, nignore) ;
if (poplistname != NULL)
{
ZALLOC(eglist, numindivs, char *) ;
numeg = loadlist(eglist, poplistname) ;
seteglist(indivmarkers, numindivs, poplistname);
}
else
{
setstatus(indivmarkers, numindivs, NULL) ;
ZALLOC(eglist, MAXPOPS, char *) ;
numeg = makeeglist(eglist, MAXPOPS, indivmarkers, numindivs) ;
}
for (i=0; i<numeg; i++)
{
/* printf("%3d %s\n",i, eglist[i]) ; */
}
nindiv=0 ;
for (i=0; i<numindivs; i++)
{
indx = indivmarkers[i] ;
if(indx -> affstatus == YES) ++nindiv ;
}
for (i=0; i<numsnps; i++)
{
cupt = snpmarkers[i] ;
chrom = cupt -> chrom ;
if ((noxdata) && (chrom == (numchrom+1))) cupt-> ignore = YES ;
if (chrom == 0) cupt -> ignore = YES ;
if (chrom > (numchrom+1)) cupt -> ignore = YES ;
}
for (i=0; i<numsnps; i++)
{
cupt = snpmarkers[i] ;
pos = nnint(cupt -> physpos) ;
if ((xchrom>0) && (cupt -> chrom != xchrom)) cupt -> ignore = YES ;
if ((xchrom > 0) && (pos < lopos)) cupt -> ignore = YES ;
if ((xchrom > 0) && (pos > hipos)) cupt -> ignore = YES ;
if (cupt -> ignore) continue ;
if (numvalidgtx(indivmarkers, cupt, YES) <= 1)
{
printf("nodata: %20s\n", cupt -> ID) ;
cupt -> ignore = YES ;
}
}
if (killr2) {
nkill = killhir2(snpmarkers, numsnps, numindivs, r2physlim, r2genlim, r2thresh) ;
if (nkill>0) printf("killhir2. number of snps killed: %d\n", nkill) ;
}
ZALLOC(vv, numindivs, int) ;
numvalidgtallind(vv, snpmarkers, numsnps, numindivs) ;
for (i=0; i<numindivs; ++i) {
if (vv[i] == 0) {
indx = indivmarkers[i] ;
indx -> ignore = YES ;
}
}
free(vv) ;
numsnps = rmsnps(snpmarkers, numsnps, NULL) ; // rid ignorable snps
if (missingmode)
{
setmiss(snpmarkers, numsnps) ;
fancynorm = NO ;
}
if (weightname != NULL)
{
weightmode = YES ;
getweights(weightname, snpmarkers, numsnps) ;
}
if (ldregress>0)
{
ZALLOC(ldvv, ldregress*numindivs, double) ;
ZALLOC(ldvv2, ldregress*numindivs, double) ;
ZALLOC(vv2, numindivs, double) ;
ZALLOC(ldmat, ldregress*ldregress, double) ;
ZALLOC(ldmat2, ldregress*ldregress, double) ;
setidmat(ldmat, ldregress) ;
vst(ldmat, ldmat, 1.0e-6, ldregress*ldregress) ;
}
ZALLOC(xindex, numindivs, int) ;
ZALLOC(xindlist, numindivs, Indiv *) ;
ZALLOC(xsnplist, numsnps, SNP *) ;
if (popsizelimit > 0)
{
setplimit(indivmarkers, numindivs, eglist, numeg, popsizelimit) ;
}
nrows = loadindx(xindlist, xindex, indivmarkers, numindivs) ;
ncols = loadsnpx(xsnplist, snpmarkers, numsnps, indivmarkers) ;
printf("number of samples used: %d number of snps used: %d\n", nrows, ncols) ;
/**
cupt = xsnplist[0] ;
for (j=0; j<nrows; ++j) {
k = xindex[j] ;
g = getgtypes(cupt, k) ;
indx = indivmarkers[k] ;
t = indxindex(eglist, numeg, indx -> egroup) ;
printf("yy1 %20s %20s %20s %d %d %d\n", cupt ->ID, indx -> ID, indx -> egroup, j, k, g) ;
}
printf("yya: ") ; printimat(xindex, 1, nrows) ;
printf("zzindxa: %s\n", indivmarkers[230] -> egroup) ;
*/
/* printf("## nrows: %d ncols %d\n", nrows, ncols) ; */
ZALLOC(xmean, ncols, double) ;
ZALLOC(xfancy, ncols, double) ;
ZALLOC(XTX, nrows*nrows, double) ;
ZALLOC(evecs, nrows*nrows, double) ;
ZALLOC(tvecs, nrows*nrows, double) ;
ZALLOC(lambda, nrows, double) ;
ZALLOC(cc, nrows, double) ;
ZALLOC(ww, nrows, double) ;
ZALLOC(badlist, nrows, int) ;
blocksize = MIN(blocksize, ncols) ;
ZALLOC(tblock, nrows*blocksize, double) ;
// xfancy is multiplier for column xmean is mean to take off
// badlist is list of rows to delete (outlier removal)
numoutiter = 1 ;
if (numoutliter>=1)
{
numoutiter = numoutliter+1 ;
ZALLOC(outinfo, nrows, OUTLINFO *) ;
for (k=0; k<nrows; k++)
{
ZALLOC(outinfo[k], 1, OUTLINFO) ;
}
/* fprintf(outlfile, "##%18s %4s %6s %9s\n", "ID", "iter","eigvec", "score") ; */
}
for (outliter = 1; outliter <= numoutiter ; ++outliter) {
if (fstonly) {
setidmat(XTX, nrows) ;
vclear(lambda, 1.0, nrows) ;
break ;
}
if (outliter>1) {
ncols = loadsnpx(xsnplist, snpmarkers, numsnps, indivmarkers) ;
}
vzero(XTX, nrows*nrows) ;
vzero(tblock, nrows*blocksize) ;
xblock = 0 ;
vzero(xmean, ncols) ;
vclear(xfancy, 1.0, ncols) ;
for (i=0; i<ncols; i++)
{
cupt = xsnplist[i] ;
chrom = cupt -> chrom ;
getcolxz(cc, cupt, xindex, nrows, i, xmean, xfancy, &n0, &n1) ;
t = MIN(n0, n1) ;
if (t <= minallelecnt) {
cupt -> ignore = YES ;
vzero(cc, nrows) ;
}
if (weightmode)
{
vst(cc, cc, xsnplist[i] -> weight, nrows) ;
}
if (ldregress>0)
{
numclear = 0 ;
for (k=1; k<= ldregress; ++k)
{
j = i-k ;
if (j<0)
{
numclear = ldregress-k+1 ;
break ;
}
cupt2 = xsnplist[j] ;
if (cupt2 -> chrom != chrom) gdis = ldlimit + 1.0 ;
else gdis = cupt -> genpos - cupt2 -> genpos ;
if (gdis>=ldlimit)
{
numclear = ldregress-k+1 ;
break ;
}
}
if (numclear>0) clearld(ldmat, ldvv, ldregress, nrows, numclear) ;
ldreg(ldmat, ldmat2, cc, vv2, ldvv, ldvv2, ldregress, nrows) ;
copyarr(ldmat2, ldmat, ldregress*ldregress) ;
copyarr(vv2, cc, nrows) ;
copyarr(ldvv2, ldvv, ldregress*nrows) ;
}
copyarr(cc, tblock+xblock*nrows, nrows) ;
++xblock ;
/** this is the key code to parallelize */
if (xblock==blocksize)
{
domult(tvecs, tblock, xblock, nrows) ;
vvp(XTX, XTX, tvecs, nrows*nrows) ;
xblock = 0 ;
vzero(tblock, nrows*blocksize) ;
}
}
if (xblock>0)
{
domult(tvecs, tblock, xblock, nrows) ;
vvp(XTX, XTX, tvecs, nrows*nrows) ;
}
symit(XTX, nrows) ;
/**
a = 0; b=0 ;
printf("zz1 %12.6f ", XTX[a*nrows+b]) ;
a = nrows-1; b=nrows-1 ;
printf(" %12.6f %15.9g\n", XTX[a*nrows+b], asum(XTX, nrows*nrows)) ;
*/
if (verbose)
{
printdiag(XTX, nrows) ;
}
y = trace(XTX, nrows) / (double) (nrows-1) ;
if (isnan(y)) fatalx("bad XTX matrix\n") ;
/* printf("trace: %9.3f\n", y) ; */
if (y<=0.0) fatalx("XTX has zero trace (perhaps no data)\n") ;
vst(XTX, XTX, 1.0/y, nrows * nrows) ;
/// mean eigenvalue is 1
eigvecs(XTX, lambda, evecs, nrows) ;
// eigenvalues are in decreasing order
if (outliter > numoutliter) break ;
// last pass skips outliers
numoutleigs = MIN(numoutleigs, nrows-1) ;
nbad = ridoutlier(evecs, nrows, numoutleigs, outlthresh, badlist, outinfo) ;
if (nbad == 0) break ;
for (i=0; i<nbad; i++)
{
j = badlist[i] ;
indx = xindlist[j] ;
outpt = outinfo[j] ;
fprintf(outlfile, "REMOVED outlier %s iter %d evec %d sigmage %.3f\n", indx -> ID, outliter, outpt -> vecno, outpt -> score) ;
indx -> ignore = YES ;
}
nrows = loadindx(xindlist, xindex, indivmarkers, numindivs) ;
printf("number of samples after outlier removal: %d\n", nrows) ;
}
if (outliername != NULL) fclose(outlfile) ;
m = numgtz(lambda, nrows) ;
/* printf("matrix rank: %d\n", m) ; */
if (m==0) fatalx("no data\n") ;
/** smartrel code */
for (i=0; i<numeigs; i++) {
y = sqrt(lambda[i]) ;
vst(ww, evecs+i*nrows, y, nrows) ;
subouter(XTX, ww, nrows) ;
}
free(tvecs) ;
n = 0 ;
ZALLOC(vecind, nrows*nrows/2, int) ;
for (i=0; i<nrows; i++) {
for (j=i+1; j<nrows; j++) {
k = i*nrows + j ;
y1 = XTX[i*nrows+i] ;
y2 = XTX[j*nrows+j] ;
y = XTX[k]/sqrt(y1*y2) ;
y += 1/(double)(nrows-1);
if (y<relthresh) continue ;
vecind[n] = k ;
evecs[n] = -y ;
++n ;
}
}
free(XTX) ;
if (n==0) {
printf("## nothing above relthresh!\n") ;
printf("##end of smartrel run\n") ;
return 0 ;
}
ZALLOC(idperm, n, int) ;
sortit(evecs, idperm, n) ;
for (i=0; i<n; i++) {
j = idperm[i] ;
k = vecind[j] ;
a = k/nrows ;
b = k%nrows ;
printf("rel: %20s ", xindlist[a] ->ID) ;
printf("%20s ", xindlist[b] ->ID) ;
printf(" %9.3f", -evecs[i]) ;
printnl() ;
}
printf("##end of smartrel run\n") ;
return 0 ;
}
/** finds maximum weight clique */
void tcliqueMaxClique(
TCLIQUE_GETNNODES((*getnnodes)), /**< user function to get the number of nodes */
TCLIQUE_GETWEIGHTS((*getweights)), /**< user function to get the node weights */
TCLIQUE_ISEDGE ((*isedge)), /**< user function to check for existence of an edge */
TCLIQUE_SELECTADJNODES((*selectadjnodes)), /**< user function to select adjacent edges */
TCLIQUE_GRAPH* tcliquegraph, /**< pointer to graph data structure that is passed to graph callbacks */
TCLIQUE_NEWSOL ((*newsol)), /**< user function to call on every new solution */
TCLIQUE_DATA* tcliquedata, /**< user data to pass to new solution callback function */
int* maxcliquenodes, /**< pointer to store nodes of the maximum weight clique */
int* nmaxcliquenodes, /**< pointer to store number of nodes in the maximum weight clique */
TCLIQUE_WEIGHT* maxcliqueweight, /**< pointer to store weight of the maximum weight clique */
TCLIQUE_WEIGHT maxfirstnodeweight, /**< maximum weight of branching nodes in level 0; 0 if not used
* for cliques with at least one fractional node) */
TCLIQUE_WEIGHT minweight, /**< lower bound for weight of generated cliques */
int maxntreenodes, /**< maximal number of nodes of b&b tree */
int backtrackfreq, /**< frequency to backtrack to first level of tree (0: no premature backtracking) */
int maxnzeroextensions, /**< maximal number of zero-valued variables extending the clique */
int fixednode, /**< node that is forced to be in the clique, or -1; must have positive weight */
TCLIQUE_STATUS* status /**< pointer to store the status of the solving call */
)
{
CLIQUEHASH* cliquehash;
const TCLIQUE_WEIGHT* weights;
int* buffer;
int* K;
int* V;
int* Vzero;
int nnodes;
int nV;
int nVzero;
int i;
BMS_CHKMEM* mem;
NBC* gsd;
TCLIQUE_Bool* iscolored;
int* curcliquenodes;
int ncurcliquenodes;
TCLIQUE_WEIGHT curcliqueweight;
int* tmpcliquenodes;
int ntreenodes;
int backtracklevel;
assert(maxcliquenodes != NULL);
assert(nmaxcliquenodes != NULL);
assert(maxcliqueweight != NULL);
assert(maxntreenodes >= 0);
assert(backtrackfreq >= 0);
assert(maxnzeroextensions >= 0);
assert(status != NULL);
*status = TCLIQUE_OPTIMAL;
/* use default graph callbacks, if NULL pointers are given */
if( getnnodes == NULL )
getnnodes = tcliqueGetNNodes;
if( getweights == NULL )
getweights = tcliqueGetWeights;
if( isedge == NULL )
isedge = tcliqueIsEdge;
if( selectadjnodes == NULL )
selectadjnodes = tcliqueSelectAdjnodes;
/* get number of nodes */
nnodes = getnnodes(tcliquegraph);
debugMessage("calculating maximal weighted clique in graph (%d nodes)\n", nnodes);
/* set up data structures */
if( newsol != NULL )
createCliquehash(&cliquehash, CLIQUEHASH_INITSIZE);
else
cliquehash = NULL;
ALLOC_ABORT( BMSallocMemoryArray(&buffer, nnodes) );
ALLOC_ABORT( BMSallocMemoryArray(&K, nnodes) );
ALLOC_ABORT( BMSallocMemoryArray(&V, nnodes) );
ALLOC_ABORT( BMSallocMemoryArray(&Vzero, nnodes) );
ALLOC_ABORT( BMSallocMemoryArray(&gsd, nnodes) );
ALLOC_ABORT( BMSallocMemoryArray(&iscolored, nnodes) );
ALLOC_ABORT( BMSallocMemoryArray(&curcliquenodes, nnodes) );
ALLOC_ABORT( BMSallocMemoryArray(&tmpcliquenodes, nnodes) );
/* set weight and number of nodes of maximum weighted clique */
*nmaxcliquenodes = 0;
*maxcliqueweight = minweight-1;
ncurcliquenodes = 0;
curcliqueweight = 0;
ntreenodes = 0;
/* set up V and Vzero */
weights = getweights(tcliquegraph);
assert(weights != NULL);
nV = 0;
nVzero = 0;
for( i = 0 ; i < nnodes; i++ )
{
if( weights[i] == 0 )
{
Vzero[nVzero] = i;
nVzero++;
}
else
{
V[nV] = i;
nV++;
}
}
/* initialize own memory allocator for coloring */
mem = BMScreateChunkMemory(sizeof(LIST_ITV), CHUNK_SIZE, -1);
/* branch to find maximum weight clique */
backtracklevel = branch(getnnodes, getweights, isedge, selectadjnodes, tcliquegraph, newsol, tcliquedata, mem,
cliquehash, buffer, 0, V, nV, Vzero, nVzero, gsd, iscolored, K, 0,
maxcliquenodes, nmaxcliquenodes, maxcliqueweight,
curcliquenodes, &ncurcliquenodes, &curcliqueweight, tmpcliquenodes,
maxfirstnodeweight, &ntreenodes, maxntreenodes, backtrackfreq, maxnzeroextensions, fixednode, status);
if( backtracklevel != INT_MAX && *status == TCLIQUE_OPTIMAL )
*status = TCLIQUE_USERABORT;
/* delete own memory allocator for coloring */
BMSdestroyChunkMemory(&mem);
/* free data structures */
BMSfreeMemoryArray(&tmpcliquenodes);
BMSfreeMemoryArray(&curcliquenodes);
BMSfreeMemoryArray(&iscolored);
BMSfreeMemoryArray(&gsd);
BMSfreeMemoryArray(&Vzero);
BMSfreeMemoryArray(&V);
BMSfreeMemoryArray(&K);
BMSfreeMemoryArray(&buffer);
if( newsol != NULL )
freeCliquehash(&cliquehash);
}
/** branches the searching tree, branching nodes are selected in decreasing order of their apriori bound,
* returns the level to which we should backtrack, or INT_MAX for continuing normally
*/
static
int branch(
TCLIQUE_GETNNODES((*getnnodes)), /**< user function to get the number of nodes */
TCLIQUE_GETWEIGHTS((*getweights)), /**< user function to get the node weights */
TCLIQUE_ISEDGE ((*isedge)), /**< user function to check for existence of an edge */
TCLIQUE_SELECTADJNODES((*selectadjnodes)), /**< user function to select adjacent edges */
TCLIQUE_GRAPH* tcliquegraph, /**< pointer to graph data structure */
TCLIQUE_NEWSOL ((*newsol)), /**< user function to call on every new solution */
TCLIQUE_DATA* tcliquedata, /**< user data to pass to user callback function */
BMS_CHKMEM* mem, /**< block memory */
CLIQUEHASH* cliquehash, /**< clique hash table */
int* buffer, /**< buffer of size nnodes */
int level, /**< level of b&b tree */
int* V, /**< non-zero weighted nodes for branching */
int nV, /**< number of non-zero weighted nodes for branching */
int* Vzero, /**< zero weighted nodes */
int nVzero, /**< number of zero weighted nodes */
NBC* gsd, /**< neighbour color information of all nodes */
TCLIQUE_Bool* iscolored, /**< coloring status of all nodes */
int* K, /**< nodes from the b&b tree */
TCLIQUE_WEIGHT weightK, /**< weight of the nodes from b&b tree */
int* maxcliquenodes, /**< pointer to store nodes of the maximum weight clique */
int* nmaxcliquenodes, /**< pointer to store number of nodes in the maximum weight clique */
TCLIQUE_WEIGHT* maxcliqueweight, /**< pointer to store weight of the maximum weight clique */
int* curcliquenodes, /**< pointer to store nodes of currenct clique */
int* ncurcliquenodes, /**< pointer to store number of nodes in current clique */
TCLIQUE_WEIGHT* curcliqueweight, /**< pointer to store weight of current clique */
int* tmpcliquenodes, /**< buffer for storing the temporary clique */
TCLIQUE_WEIGHT maxfirstnodeweight, /**< maximum weight of branching nodes in level 0; 0 if not used
** (for cliques with at least one fractional node) */
int* ntreenodes, /**< pointer to store number of nodes of b&b tree */
int maxntreenodes, /**< maximal number of nodes of b&b tree */
int backtrackfreq, /**< frequency to backtrack to first level of tree (0: no premature backtracking) */
int maxnzeroextensions, /**< maximal number of zero-valued variables extending the clique */
int fixednode, /**< node that is forced to be in the clique, or -1; must have positive weight */
TCLIQUE_STATUS* status /**< pointer to store the status of the solving call */
)
{
TCLIQUE_Bool isleaf;
const TCLIQUE_WEIGHT* weights;
TCLIQUE_WEIGHT* apbound;
TCLIQUE_WEIGHT subgraphweight;
TCLIQUE_WEIGHT weightKold;
TCLIQUE_WEIGHT tmpcliqueweight;
int backtracklevel;
int ntmpcliquenodes;
int i;
assert(getnnodes != NULL);
assert(getweights != NULL);
assert(selectadjnodes != NULL);
assert(mem != NULL);
assert(V != NULL);
assert(gsd != NULL);
assert(iscolored != NULL);
assert(K != NULL);
assert(maxcliqueweight != NULL);
assert(curcliquenodes != NULL);
assert(ncurcliquenodes != NULL);
assert(curcliqueweight != NULL);
assert(ntreenodes != NULL);
assert(maxfirstnodeweight >= 0);
assert(*ntreenodes >= 0);
assert(maxntreenodes >= 0);
assert(status != NULL);
/* increase the number of nodes, and stop solving, if the node limit is exceeded */
(*ntreenodes)++;
#ifdef TCLIQUE_DEBUG
debugMessage("(level %d, treenode %d) maxclique = %d, curclique = %d [mem=%lld (%lld), cliques=%d]\n",
level, *ntreenodes, *maxcliqueweight, *curcliqueweight,
BMSgetChunkMemoryUsed(mem), BMSgetMemoryUsed(), cliquehash == NULL ? 0 : cliquehash->ncliques);
debugMessage(" -> current branching (weight %d):", weightK);
for( i = 0; i < level; ++i )
debugPrintf(" %d", K[i]);
debugPrintf("\n");
debugMessage(" -> branching candidates:");
for( i = 0; i < nV; ++i )
debugPrintf(" %d", V[i]);
debugPrintf("\n");
#endif
if( *ntreenodes > maxntreenodes )
{
*status = TCLIQUE_NODELIMIT;
return TRUE;
}
weights = getweights(tcliquegraph);
backtracklevel = INT_MAX;
isleaf = TRUE;
/* allocate temporary memory for a priori bounds */
ALLOC_ABORT( BMSallocMemoryArray(&apbound, nV) );
BMSclearMemoryArray(apbound, nV);
/* use coloring relaxation to generate an upper bound for the current subtree and a heuristic solution */
subgraphweight = boundSubgraph(getnnodes, getweights, isedge, selectadjnodes, tcliquegraph,
mem, buffer, V, nV, gsd, iscolored, apbound,
tmpcliquenodes, &ntmpcliquenodes, &tmpcliqueweight);
#ifndef NDEBUG
/* check correctness of V and apbound arrays */
for( i = 0; i < nV; ++i )
{
assert(0 <= V[i] && V[i] < getnnodes(tcliquegraph));
assert(i == 0 || V[i-1] < V[i]);
assert(apbound[i] >= 0);
assert((apbound[i] == 0) == (weights[V[i]] == 0));
}
#endif
/* check, whether the heuristic solution is better than the current subtree's solution;
* if the user wanted to have a fixed variable inside the clique and we are in level 0, we first have to
* fix this variable in this level (the current clique might not contain the fixed node)
*/
if( weightK + tmpcliqueweight > *curcliqueweight && (level > 0 || fixednode == -1) )
{
/* install the newly generated clique as current clique */
for( i = 0; i < level; ++i )
curcliquenodes[i] = K[i];
for( i = 0; i < ntmpcliquenodes; ++i )
curcliquenodes[level+i] = tmpcliquenodes[i];
*ncurcliquenodes = level + ntmpcliquenodes;
*curcliqueweight = weightK + tmpcliqueweight;
#ifdef TCLIQUE_DEBUG
debugMessage(" -> new current clique with weight %d at node %d in level %d:",
*curcliqueweight, *ntreenodes, level);
for( i = 0; i < *ncurcliquenodes; ++i )
debugPrintf(" %d", curcliquenodes[i]);
debugPrintf("\n");
#endif
}
/* discard subtree, if the upper bound is not better than the weight of the currently best clique;
* if only 2 nodes are left, the maximal weighted clique was already calculated in boundSubgraph() and nothing
* more has to be done;
* however, if the user wanted to have a fixed node and we are in the first decision level, we have to continue
*/
if( weightK + subgraphweight > *maxcliqueweight && (nV > 2 || (fixednode >= 0 && level == 0)) )
{
int* Vcurrent;
int nVcurrent;
int nValive;
int branchingnode;
assert(nV > 0);
/* process current subtree */
level++;
/* set up data structures */
ALLOC_ABORT( BMSallocMemoryArray(&Vcurrent, nV-1) );
nValive = nV;
weightKold = weightK;
debugMessage("============================ branching level %d ===============================\n", level);
/* branch on the nodes of V by decreasing order of their apriori bound */
while( backtracklevel >= level && nValive > 0 )
{
int branchidx;
/* check if we meet the backtracking frequency - in this case abort the search until we have reached first level */
if( level > 1 && backtrackfreq > 0 && (*ntreenodes) % backtrackfreq == 0 )
{
backtracklevel = 1;
break;
}
/* get next branching node */
if( level == 1 && fixednode >= 0 )
{
/* select the fixed node as first "branching" candidate */
for( branchidx = 0; branchidx < nValive && V[branchidx] != fixednode; branchidx++ )
{}
assert(branchidx < nValive);
assert(V[branchidx] == fixednode);
}
else if( level == 1 && maxfirstnodeweight > 0 )
branchidx = getMaxApBoundIndexNotMaxWeight(V, nValive, apbound, weights, maxfirstnodeweight);
else
branchidx = getMaxApBoundIndex(nValive, apbound);
if( branchidx < 0 )
break;
assert(0 <= branchidx && branchidx < nValive && nValive <= nV);
assert(apbound[branchidx] > 0);
assert(weights[V[branchidx]] > 0);
/* test a priori bound */
if( (weightKold + apbound[branchidx]) <= *maxcliqueweight )
break;
debugMessage("%d. branching in level %d (treenode %d): bidx=%d, node %d, weight %d, upperbound: %d+%d = %d, maxclique=%d\n",
nV-nValive+1, level, *ntreenodes, branchidx, V[branchidx], weights[V[branchidx]], weightKold,
apbound[branchidx], weightKold + apbound[branchidx], *maxcliqueweight);
/* because we branch on this node, the node is no leaf in the tree */
isleaf = FALSE;
/* update the set of nodes from the b&b tree
* K = K & {branchingnode}
*/
branchingnode = V[branchidx];
K[level-1] = branchingnode;
weightK = weightKold + weights[branchingnode];
/* update the set of nodes for branching
* V = V \ {branchingnode}
*/
nValive--;
for( i = branchidx; i < nValive; ++i )
{
V[i] = V[i+1];
apbound[i] = apbound[i+1];
}
/* set the nodes for the next level of b&b tree
* Vcurrent = nodes of V, that are adjacent to branchingnode
*/
nVcurrent = selectadjnodes(tcliquegraph, branchingnode, V, nValive, Vcurrent);
/* process the selected subtree */
backtracklevel = branch(getnnodes, getweights, isedge, selectadjnodes, tcliquegraph, newsol, tcliquedata,
mem, cliquehash, buffer,
level, Vcurrent, nVcurrent, Vzero, nVzero, gsd, iscolored, K, weightK,
maxcliquenodes, nmaxcliquenodes, maxcliqueweight,
curcliquenodes, ncurcliquenodes, curcliqueweight, tmpcliquenodes,
maxfirstnodeweight, ntreenodes, maxntreenodes, backtrackfreq, maxnzeroextensions, -1, status);
/* if all other candidates stayed in the candidate list, the current branching was optimal and
* there is no need to try the remaining ones
*/
if( nVcurrent == nValive )
{
debugMessage("branching on node %d was optimal - ignoring remaining candidates\n", branchingnode);
nValive = 0;
}
/* if we had a fixed node, ignore all other nodes */
if( fixednode >= 0 )
nValive = 0;
}
debugMessage("========================== branching level %d end =============================\n\n", level);
/* free data structures */
BMSfreeMemoryArray(&Vcurrent);
}
/* check, whether any branchings have been applied, or if this node is a leaf of the branching tree */
if( isleaf )
{
/* the current clique is the best clique found on the path to this leaf
* -> check, whether it is an improvement to the currently best clique
*/
if( *curcliqueweight > *maxcliqueweight )
{
TCLIQUE_Bool stopsolving;
debugMessage("found clique of weight %d at node %d in level %d\n", *curcliqueweight, *ntreenodes, level);
newSolution(selectadjnodes, tcliquegraph, newsol, tcliquedata, cliquehash, buffer, Vzero, nVzero,
maxnzeroextensions, curcliquenodes, *ncurcliquenodes, *curcliqueweight,
maxcliquenodes, nmaxcliquenodes, maxcliqueweight, &stopsolving);
if( stopsolving )
{
debugMessage(" -> solving terminated by callback method\n");
backtracklevel = 0;
}
}
/* discard the current clique */
*ncurcliquenodes = 0;
*curcliqueweight = 0;
}
#ifdef TCLIQUE_DEBUG
if( level > backtracklevel )
{
debugMessage("premature backtracking after %d nodes - level %d\n", *ntreenodes, level);
}
#endif
/* free data structures */
BMSfreeMemoryArray(&apbound);
return backtracklevel;
}
/** tries to find a clique, if V has only one or two nodes */
static
void reduced(
TCLIQUE_GETWEIGHTS((*getweights)), /**< user function to get the node weights */
TCLIQUE_ISEDGE ((*isedge)), /**< user function to check for existence of an edge */
TCLIQUE_GRAPH* tcliquegraph, /**< pointer to graph data structure */
int* V, /**< non-zero weighted nodes for branching */
int nV, /**< number of non-zero weighted nodes for branching */
TCLIQUE_WEIGHT* apbound, /**< apriori bound of nodes for branching */
int* tmpcliquenodes, /**< buffer for storing the temporary clique */
int* ntmpcliquenodes, /**< pointer to store number of nodes of the temporary clique */
TCLIQUE_WEIGHT* tmpcliqueweight /**< pointer to store weight of the temporary clique */
)
{
const TCLIQUE_WEIGHT* weights;
assert(getweights != NULL);
assert(isedge != NULL);
assert(tcliquegraph != NULL);
assert(V != NULL);
assert(0 <= nV && nV <= 2);
assert(apbound != NULL);
assert(tmpcliquenodes != NULL);
assert(ntmpcliquenodes != NULL);
assert(tmpcliqueweight != NULL);
weights = getweights(tcliquegraph);
assert(nV == 0 || weights[V[0]] > 0);
assert(nV <= 1 || weights[V[1]] > 0);
if( nV >= 1 )
apbound[0] = weights[V[0]];
if( nV >= 2 )
apbound[1] = weights[V[1]];
/* check if nodes are adjacent */
if( nV >= 2 && isedge(tcliquegraph, V[0], V[1]) )
{
assert(isedge(tcliquegraph, V[1], V[0]));
/* put nodes into clique */
tmpcliquenodes[0] = V[0];
tmpcliquenodes[1] = V[1];
*ntmpcliquenodes = 2;
*tmpcliqueweight = weights[V[0]] + weights[V[1]];
apbound[0] += weights[V[1]];
}
else if( nV >= 2 && weights[V[1]] > weights[V[0]] )
{
/* put V[1] into clique */
tmpcliquenodes[0] = V[1];
*ntmpcliquenodes = 1;
*tmpcliqueweight = weights[V[1]];
}
else if( nV >= 1 )
{
/* put V[0] into clique */
tmpcliquenodes[0] = V[0];
*ntmpcliquenodes = 1;
*tmpcliqueweight = weights[V[0]];
}
else
{
*tmpcliqueweight = 0;
*ntmpcliquenodes = 0;
}
}
/** colors the positive weighted nodes of a given set of nodes V with the lowest possible number of colors and
* finds a clique in the graph induced by V, an upper bound and an apriori bound for further branching steps
*/
TCLIQUE_WEIGHT tcliqueColoring(
TCLIQUE_GETNNODES((*getnnodes)), /**< user function to get the number of nodes */
TCLIQUE_GETWEIGHTS((*getweights)), /**< user function to get the node weights */
TCLIQUE_SELECTADJNODES((*selectadjnodes)), /**< user function to select adjacent edges */
TCLIQUE_GRAPH* tcliquegraph, /**< pointer to graph data structure */
BMS_CHKMEM* mem, /**< block memory */
int* buffer, /**< buffer of size nnodes */
int* V, /**< non-zero weighted nodes for branching */
int nV, /**< number of non-zero weighted nodes for branching */
NBC* gsd, /**< neighbor color information of all nodes */
TCLIQUE_Bool* iscolored, /**< coloring status of all nodes */
TCLIQUE_WEIGHT* apbound, /**< pointer to store apriori bound of nodes for branching */
int* clique, /**< buffer for storing the clique */
int* nclique, /**< pointer to store number of nodes in the clique */
TCLIQUE_WEIGHT* weightclique /**< pointer to store the weight of the clique */
)
{
const TCLIQUE_WEIGHT* weights;
TCLIQUE_WEIGHT maxsatdegree;
TCLIQUE_WEIGHT range;
TCLIQUE_Bool growclique;
int node;
int nodeVindex;
int i;
int j;
LIST_ITV* colorinterval;
LIST_ITV nwcitv;
LIST_ITV* pnc;
LIST_ITV* lcitv;
LIST_ITV* item;
LIST_ITV* tmpitem;
int* workclique;
int* currentclique;
int ncurrentclique;
int weightcurrentclique;
int* Vadj;
int nVadj;
int adjidx;
assert(getnnodes != NULL);
assert(getweights != NULL);
assert(selectadjnodes != NULL);
assert(buffer != NULL);
assert(V != NULL);
assert(nV > 0);
assert(clique != NULL);
assert(nclique != NULL);
assert(weightclique != NULL);
assert(gsd != NULL);
assert(iscolored != NULL);
weights = getweights(tcliquegraph);
assert(weights != NULL);
/* initialize maximum weight clique found so far */
growclique = TRUE;
*nclique = 0;
*weightclique = 0;
/* get node of V with maximum weight */
nodeVindex = getMaxWeightIndex(getnnodes, getweights, tcliquegraph, V, nV);
node = V[nodeVindex];
assert(0 <= node && node < getnnodes(tcliquegraph));
range = weights[node];
assert(range > 0);
/* set up data structures for coloring */
BMSclearMemoryArray(iscolored, nV); /* new-memory */
BMSclearMemoryArray(gsd, nV); /* new-memory */
iscolored[nodeVindex] = TRUE;
/* color the first node */
debugMessage("---------------coloring-----------------\n");
debugMessage("1. node choosen: vindex=%d, vertex=%d, satdeg=%d, range=%d)\n",
nodeVindex, node, gsd[nodeVindex].satdeg, range);
/* set apriori bound: apbound(v_i) = satdeg(v_i) + weight(v_i) */
apbound[nodeVindex] = range;
assert(apbound[nodeVindex] > 0);
/* update maximum saturation degree: maxsatdeg = max { satdeg(v_i) + weight(v_i) | v_i in V } */
maxsatdegree = range;
debugMessage("-> updated neighbors:\n");
/* set neighbor color of the adjacent nodes of node */
Vadj = buffer;
nVadj = selectadjnodes(tcliquegraph, node, V, nV, Vadj);
for( i = 0, adjidx = 0; i < nV && adjidx < nVadj; ++i )
{
assert(V[i] <= Vadj[adjidx]); /* Vadj is a subset of V */
if( V[i] == Vadj[adjidx] )
{
/* node is adjacent to itself, but we do not need to color it again */
if( i == nodeVindex )
{
/* go to the next node in Vadj */
adjidx++;
continue;
}
debugMessage(" nodeVindex=%d, node=%d, weight=%d, satdegold=%d -> ",
i, V[i], weights[V[i]], gsd[i].satdeg);
/* sets satdeg for adjacent node */
gsd[i].satdeg = range;
/* creates new color interval [1,range] */
ALLOC_ABORT( BMSallocChunkMemory(mem, &colorinterval) );
colorinterval->next = NULL;
colorinterval->itv.inf = 1;
colorinterval->itv.sup = range;
/* colorinterval is the first added element of the list of neighborcolors of the adjacent node */
gsd[i].lcitv = colorinterval;
/* go to the next node in Vadj */
adjidx++;
debugPrintf("satdegnew=%d, nbc=[%d,%d]\n", gsd[i].satdeg, gsd[i].lcitv->itv.inf, gsd[i].lcitv->itv.sup);
}
}
/* set up data structures for the current clique */
ALLOC_ABORT( BMSallocMemoryArray(¤tclique, nV) );
workclique = clique;
/* add node to the current clique */
currentclique[0] = node;
ncurrentclique = 1;
weightcurrentclique = range;
/* color all other nodes of V */
for( i = 0 ; i < nV-1; i++ )
{
assert((workclique == clique) != (currentclique == clique));
/* selects the next uncolored node to color */
nodeVindex = getMaxSatdegIndex(V, nV, gsd, iscolored, weights);
if( nodeVindex == -1 ) /* no uncolored nodes left */
break;
node = V[nodeVindex];
assert(0 <= node && node < getnnodes(tcliquegraph));
range = weights[node];
assert(range > 0);
iscolored[nodeVindex] = TRUE;
debugMessage("%d. node choosen: vindex=%d, vertex=%d, satdeg=%d, range=%d, growclique=%u, weight=%d)\n",
i+2, nodeVindex, node, gsd[nodeVindex].satdeg, range, growclique, weightcurrentclique);
/* set apriori bound: apbound(v_i) = satdeg(v_i) + weight(v_i) */
apbound[nodeVindex] = gsd[nodeVindex].satdeg + range;
assert(apbound[nodeVindex] > 0);
/* update maximum saturation degree: maxsatdeg = max { satdeg(v_i) + weight(v_i) | v_i in V } */
if( maxsatdegree < apbound[nodeVindex] )
maxsatdegree = apbound[nodeVindex];
/* update clique */
if( gsd[nodeVindex].satdeg == 0 )
{
/* current node is not adjacent to nodes of current clique,
* i.e. current clique can not be increased
*/
debugMessage("current node not adjacend to current clique (weight:%d) -> starting new clique\n",
weightcurrentclique);
/* check, if weight of current clique is larger than weight of maximum weight clique found so far */
if( weightcurrentclique > *weightclique )
{
int* tmp;
/* update maximum weight clique found so far */
assert((workclique == clique) != (currentclique == clique));
tmp = workclique;
*weightclique = weightcurrentclique;
*nclique = ncurrentclique;
workclique = currentclique;
currentclique = tmp;
assert((workclique == clique) != (currentclique == clique));
}
weightcurrentclique = 0;
ncurrentclique = 0;
growclique = TRUE;
}
if( growclique )
{
/* check, if the current node is still adjacent to all nodes in the clique */
if( gsd[nodeVindex].satdeg == weightcurrentclique )
{
assert(ncurrentclique < nV);
currentclique[ncurrentclique] = node;
ncurrentclique++;
weightcurrentclique += range;
#ifdef TCLIQUE_DEBUG
{
int k;
debugMessage("current clique (size:%d, weight:%d):", ncurrentclique, weightcurrentclique);
for( k = 0; k < ncurrentclique; ++k )
debugPrintf(" %d", currentclique[k]);
debugPrintf("\n");
}
#endif
}
else
{
debugMessage("node satdeg: %d, clique weight: %d -> stop growing clique\n",
gsd[nodeVindex].satdeg, weightcurrentclique);
growclique = FALSE;
}
}
/* search for fitting color intervals for current node */
pnc = &nwcitv;
if( gsd[nodeVindex].lcitv == NULL )
{
/* current node has no colored neighbors yet: create new color interval [1,range] */
ALLOC_ABORT( BMSallocChunkMemory(mem, &colorinterval) );
colorinterval->next = NULL;
colorinterval->itv.inf = 1;
colorinterval->itv.sup = range;
/* add the new colorinterval [1, range] to the list of chosen colorintervals for node */
pnc->next = colorinterval;
pnc = colorinterval;
}
else
{
int tocolor;
int dif;
/* current node has colored neighbors */
tocolor = range;
lcitv = gsd[nodeVindex].lcitv;
/* check, if first neighbor color interval [inf, sup] has inf > 1 */
if( lcitv->itv.inf != 1 )
{
/* create new interval [1, min{range, inf}] */
dif = lcitv->itv.inf - 1 ;
if( dif > tocolor )
dif = tocolor;
ALLOC_ABORT( BMSallocChunkMemory(mem, &colorinterval) );
colorinterval->next = NULL;
colorinterval->itv.inf = 1;
colorinterval->itv.sup = dif;
tocolor -= dif;
pnc->next = colorinterval;
pnc = colorinterval;
}
/* as long as node is not colored with all colors, create new color interval by filling
* the gaps in the existing neighbor color intervals of the neighbors of node
*/
while( tocolor > 0 )
{
dif = tocolor;
ALLOC_ABORT( BMSallocChunkMemory(mem, &colorinterval) );
colorinterval->next = NULL;
colorinterval->itv.inf = lcitv->itv.sup+1;
if( lcitv->next != NULL )
{
int min;
min = lcitv->next->itv.inf - lcitv->itv.sup - 1;
if( dif > min )
dif = min;
lcitv = lcitv->next;
}
colorinterval->itv.sup = colorinterval->itv.inf + dif - 1;
tocolor -= dif;
pnc->next = colorinterval;
pnc = colorinterval;
}
}
debugMessage("-> updated neighbors:\n");
/* update saturation degree and neighbor colorintervals of all neighbors of node */
Vadj = buffer;
nVadj = selectadjnodes(tcliquegraph, node, V, nV, Vadj);
for( j = 0, adjidx = 0; j < nV && adjidx < nVadj; ++j )
{
assert(V[j] <= Vadj[adjidx]); /* Vadj is a subset of V */
if( V[j] == Vadj[adjidx] )
{
if( !iscolored[j] )
{
debugMessage(" nodeVindex=%d, node=%d, weight=%d, satdegold=%d -> ",
j, V[j], weights[V[j]], gsd[j].satdeg);
updateNeighbor(mem, &gsd[j], nwcitv.next);
debugPrintf("satdegnew=%d, nbc=[%d,%d]\n", gsd[j].satdeg, gsd[j].lcitv->itv.inf, gsd[j].lcitv->itv.sup);
}
/* go to the next node in Vadj */
adjidx++;
}
}
/* free data structure of created colorintervals */
item = nwcitv.next;
while( item != NULL )
{
tmpitem = item->next;
BMSfreeChunkMemory(mem, &item);
item = tmpitem;
}
/* free data structure of neighbor colorinterval of node just colored */
item = gsd[nodeVindex].lcitv;
while( item != NULL )
{
tmpitem = item->next;
BMSfreeChunkMemory(mem, &item);
item = tmpitem;
}
}
assert((workclique == clique) != (currentclique == clique));
/* update maximum weight clique found so far */
if( weightcurrentclique > *weightclique )
{
int* tmp;
tmp = workclique;
*weightclique = weightcurrentclique;
*nclique = ncurrentclique;
workclique = currentclique;
currentclique = tmp;
}
assert((workclique == clique) != (currentclique == clique));
/* move the found clique to the provided clique pointer, if it is not the memory array */
if( workclique != clique )
{
assert(clique == currentclique);
assert(*nclique <= nV);
BMScopyMemoryArray(clique, workclique, *nclique);
currentclique = workclique;
}
/* free data structures */
BMSfreeMemoryArray(¤tclique);
/* clear chunk memory */
BMSclearChunkMemory(mem);
debugMessage("------------coloringend-----------------\n");
return maxsatdegree;
}
