void ldndate(int dnptr){
int i,s,sn,lptr,c,g,splflag,ptr,tmp,ldtmp,g2;
kosquare = kosave[dnptr];
s = mvs[dnptr];
if(s == PASS){ /* pass */
return;
}
g = board[s];
c = grcolor[g];
splflag = FALSE;
board[s] = NOGROUP;
if(mvconn[dnptr] != EOL){
ptr = mvconn[dnptr]; /* bring back combined groups */
g = lsplit(ptr,g);
splflag = TRUE;
}
for(ptr = mvcapt[dnptr]; ptr != EOL; ptr = links[ptr]){
g2 = list[ptr]; /* bring back killed groups */
lresurrect(g2); /* resurrect enemy group */
}
if(!splflag){ /* remove piece from group */
grsize[g]--;
if(grsize[g] == 0){ /* only one piece in group */
--maxgr; /* delete group */
killist(&grlbp[g]); /* return liberties to free list */
lptr = grnbp[g];
while(lptr != EOL){
dellist(g,&grnbp[list[lptr]]);
lptr = links[lptr];
}
if(grnbp[g] != EOL)
killist(&grnbp[g]); /* return neighbors to free list */
}
else { /* take piece away from group */
grpieces[g] = mvnext[grpieces[g]];
ptr = lbply[dnptr];
while(ptr != EOL){
dellist(list[ptr],&grlbp[g]);
--grlibs[g];
ptr = links[ptr];
}
killist(&lbply[dnptr]);
ptr = nbply[dnptr];
while(ptr != EOL){
tmp = list[ptr];
dellist(tmp,&grnbp[g]);
dellist(g,&grnbp[tmp]);
ptr = links[ptr];
}
if(nbply[dnptr] != EOL)
killist(&nbply[dnptr]);
}
if(edge[s] < 2){
i = fdir[s];
for(ldtmp = ldir[i]; i < ldtmp; ++i){
sn = s + nbr[i];
--lnbf[sn][c];
++lnbn[sn];
addlist(s,&nblbp[sn]);
g = board[sn];
if(g == NOGROUP)continue;
if(addlist(s,&grlbp[g])){
++grlibs[g];
}
}
}
else{
--lnbf[s+1][c];
++lnbn[s+1];
addlist(s,&nblbp[s+1]);
--lnbf[s-1][c];
++lnbn[s-1];
addlist(s,&nblbp[s-1]);
--lnbf[s+boardsize][c];
++lnbn[s+boardsize];
addlist(s,&nblbp[s+boardsize]);
--lnbf[s-boardsize][c];
++lnbn[s-boardsize];
addlist(s,&nblbp[s-boardsize]);
g = board[s+1];
if(g != NOGROUP )
if(addlist(s,&grlbp[g]))++grlibs[g];
g = board[s-1];
if(g != NOGROUP )
if(addlist(s,&grlbp[g]))++grlibs[g];
g = board[s+boardsize];
if(g != NOGROUP )
if(addlist(s,&grlbp[g]))++grlibs[g];
g = board[s-boardsize];
if(g != NOGROUP )
if(addlist(s,&grlbp[g]))++grlibs[g];
}
}
else {
if(edge[s] < 2){
i = fdir[s];
for(ldtmp = ldir[i]; i < ldtmp; ++i){
sn = s + nbr[i];
--lnbf[sn][c];
++lnbn[sn];
addlist(s,&nblbp[sn]);
g = board[sn];
if(grcolor[g] != 1-c)continue;
if(addlist(s,&grlbp[g])){
++grlibs[g];
}
}
}
else{
--lnbf[s+1][c];
++lnbn[s+1];
addlist(s,&nblbp[s+1]);
--lnbf[s-1][c];
++lnbn[s-1];
addlist(s,&nblbp[s-1]);
--lnbf[s+boardsize][c];
++lnbn[s+boardsize];
addlist(s,&nblbp[s+boardsize]);
--lnbf[s-boardsize][c];
++lnbn[s-boardsize];
addlist(s,&nblbp[s-boardsize]);
g = board[s+1];
if(grcolor[g] == 1-c)
if(addlist(s,&grlbp[g]))++grlibs[g];
g = board[s-1];
if(grcolor[g] == 1-c)
if(addlist(s,&grlbp[g]))++grlibs[g];
g = board[s+boardsize];
if(grcolor[g] == 1-c)
if(addlist(s,&grlbp[g]))++grlibs[g];
g = board[s-boardsize];
if(grcolor[g] == 1-c)
if(addlist(s,&grlbp[g]))++grlibs[g];
}
}
}
int main(int argc,char* argv[])
{
list<string> genes;
DictStringSet gene_mutatedSamples;
ifstream sample_mut_f;
ifstream analyzed_genes_file;
ofstream most_visited_file;
ofstream highest_weight_file;
int K;
int mAS_perGene;
int num_iterations;
set<string> all_samples;
DictStringSet sample_mutatedGenes;
int num_exper;
int step_length;
string sampleID;
if(argc < 8)
{
cout << "Usage: python Dendrix.py mutations_file K minFreqGene number_iterations analyzed_genes_file num_exper step_length\n";
cout << "mutations_file: input file with mutation matrix (see README.txt for description)\n";
cout << "K: size of the sets to be sampled\n";
cout << "minFreqGene: minimum frequency of mutation for a gene to be considered in the analysis\n";
cout << "number_iterations: number of iterations of the MCMC\n";
cout << "analyzed_genes_file: file with list of analyzed genes (see README.txt for description)\n";
cout << "num_exper: number of times the experiment is going to be run (see README.txt for description)\n";
cout << "step_length: number of iterations of the MCMC between two samples\n";
exit(0);
}
genes.clear();
gene_mutatedSamples.clear();
sample_mut_f.open(argv[1]);
K = atoi(argv[2]);
mAS_perGene = atoi(argv[3]);
num_iterations = atoi(argv[4]);
analyzed_genes_file.open(argv[5]);
all_samples.clear();
sample_mutatedGenes.clear();
num_exper = atoi(argv[6]);
step_length = atoi(argv[7]);
printf("Load genes...\n");
string line;
list<string> v;
while(!analyzed_genes_file.eof())
{
getline(analyzed_genes_file,line);
lsplit(line,v);
if(!v.empty())
{
genes.push_back(v.front());
gene_mutatedSamples[v.front()] = set<string>();
}
v.clear();
}
// genes.pop_back();
gene_mutatedSamples.erase("");
analyzed_genes_file.close();
printf("Loading Mutations...\n");
vector<string> vv;
while(!sample_mut_f.eof())
{
getline(sample_mut_f,line);
if(line.empty())
break;
vsplit(line,vv);
sampleID = vv[0];
all_samples.insert(sampleID);
sample_mutatedGenes[sampleID] = set<string>();
for (int i = 0; i < (sz(vv) - 1); ++i)
{
string gene = vv[i+1];
if(cpresent(genes,gene))
{
if(!present(gene_mutatedSamples,gene))
gene_mutatedSamples[gene] = set<string>();
gene_mutatedSamples[gene].insert(sampleID);
sample_mutatedGenes[sampleID].insert(gene);
}
}
vv.clear();
}
sample_mut_f.close();
DictStringDouble sample_numMut;
tr(sample_mutatedGenes,it)
{
// it->first refers to the sampleID or PatientID
unsigned tmp_numMut = sample_mutatedGenes[it->first].size();
sample_numMut[it->first] = (double)tmp_numMut;
}
