int main(int argc, char* argv[]) {
if (argc < 3) {
cout << "Needs 3 arguments: 1) file with pairwise distances between elements. ";
cout << "File should be 3 tab separated columns with 1 undirected edge per line of the format node1, node2, edgeWeight (similarity between node1 and node2)" << endl;
cout << "2) threshold between clusters (alpha parameter)" << endl;
cout << "3) merge density for overlapping clusters (beta parameter. Optional with default = 0.5)" << endl;
cout << "4) name for terminal node (i.e. gene, patient, etc.). Optional with default = gene" << endl;
return 0;
}
Corrector::initialize();
/*for (unsigned i = 0; i < 600; ++i) {
cout << i << "\t" << Corrector::correction(i) << endl;
}
return 1;*/
map<string, unsigned> nodeNamesToIDs;
// Load input network graphs
string netFile = argv[1];
double threshold = stod(argv[2]);
double density = 0.5;
if (argc >= 4) {
density = stod(argv[3]);
}
string terminalName = "gene";
if (argc >= 5) {
terminalName = string(argv[4]);
}
time_t start, end;
time(&start);
cout << "# Loading input network graph" << endl;
graph_undirected inputNetwork(netFile, nodeNamesToIDs);
time(&end);
double dif = difftime(end,start);
cout << "# Loading input network took " << dif << " seconds" << endl;
// Create ontology from other networks
cout << "# Clique finding beginning" << endl;
DAGraph ontology;
ontology.setTerminalName(terminalName);
nodeDistanceObject nodeDistances;
time (&start);
dagConstruct::constructDAG(inputNetwork, ontology, nodeDistances, threshold, density);
time (&end);
dif = difftime(end,start);
cout << "# Ontology construction took " << dif << " seconds" << endl;
cout << "# Ontology is: " << endl;
for(map< pair<unsigned,unsigned>, string >::iterator edgesIt = ontology.edgesBegin(); edgesIt != ontology.edgesEnd(); ++edgesIt) {
// THIS VERSION GIVES THE DISTANCE BETWEEN POINTS
//cout << ontology.getName(edgesIt->first.first) << "\t" << ontology.getName(edgesIt->first.second) << "\t" << edgesIt->second << "\t" << (ontology.getWeight(edgesIt->first.second) - ontology.getWeight(edgesIt->first.first)) / 2.0 << endl;
// THIS VERSION JUST TELLS THE WEIGHT ON THE PARENT TERM
cout << ontology.getName(edgesIt->first.first) << "\t" << ontology.getName(edgesIt->first.second) << "\t" << edgesIt->second << "\t" << ontology.getWeight(edgesIt->first.first) << endl;
}
return 1;
}
void readRouter()
{
////FILE * datafile;
FILE * outfile;
struct network* target;
////int id1;
////int id2;
////double weight;
////int error;
////int totalNum;
struct netInfo* netinfo;
struct CLSTS* clsts;
FILE * pFile_node;
FILE * pFile_pajek;
// 2) analyze the properties
target=NULL;
outfile=fopen("./realdata/Router_net.txt", "r");
inputNetwork(&target, outfile);
fclose (outfile);
printf("\n %d %d \n", target->nodeNum, target->linkNum);
// getNetwork Info
netinfo=(struct netInfo*)mem_alloc(sizeof(struct netInfo));
initNetInfo(netinfo, target);
getBasicNetInfo(target, netinfo);
clsts=NULL;
getCLSTS(target,&clsts);
getClstNetInfo(target, clsts, netinfo);
pFile_node=fopen("Router_node.txt", "w");
outputNodeInfo(netinfo, pFile_node);
fclose (pFile_node);
// statis info
pFile_pajek=fopen("Router_pajek.txt", "w");
outputNetwork_pajek( target, pFile_pajek);
fclose (pFile_pajek);
printf(" %.5f %d %.5f %.5f %d %.5f %.5f %d %.5f %.5f \n",
netinfo->av_k,
netinfo->max_k,
netinfo->av_coef,
netinfo->e_loc,
netinfo->S_size,
netinfo->av_s,
netinfo->S_avspl,
netinfo->S_maxspl,
netinfo->e_glob_active,
netinfo->S_e_glob);
freeNetwork(target);
freeCLSTS(clsts);
freeNetInfo(netinfo);
}
int
readSCN(char * netfile) /*input: name of file recording network information*/
{
int error;
FILE *infile;
time_t time_begin,time_end;
struct tm * TM ;
char dir_p[10];
int name_size;
static struct network * scn;
/* 1) from files, get the header dependency network and filelist*/
error=0;
name_size=30;
infile=fopen(netfile, "r");
if(infile==NULL)
{
printf("file \" %s \" not exist!\n", netfile);
return 1;
}
inputNetwork(&scn, infile);
fclose(infile);
/* 2) get statistical properties of the network, and record all the information into output files */
// create ouput directories
time(&time_begin);
TM=localtime(&time_begin);
strftime(dir_p, name_size, "%y%m%d%H%M", TM);
strcat(dir_p,"/");
#if defined(_WIN32)
error=_mkdir(dir_p);
#else
error=mkdir(dir_p, 0777);
#endif
analyzeSCN(scn,dir_p);
time(&time_end);
printf("\n exhausted time: %ld \n",time_end-time_begin);
//showNetwork(file_net);
/* 3) free file network, file list and other memory*/
freeNetwork(scn);
printf("\n ok! \n");
return error;
}
/*
input output network test
*/
void
ioNetwork()
{
int m0,m,step,iter;
FILE *in, *out;
time_t time_begin,time_end;
struct network * target=NULL;
struct network * newNet=NULL;
time(&time_begin);
out=fopen("net.txt","w");
step=5;
m0=m=2;
iter=1;
m=m;
m0=m0;
target=NULL;
newNet=NULL;
target=(struct network *)mem_alloc(sizeof(struct network));
baModel_o(target, m0, m, step);
printf(" the original network: \n");
showNetwork(target);
outputNetwork(target, out);
fclose(out);
in=fopen("net.txt","r");
inputNetwork(&newNet, in);
fclose(in);
printf(" the read-in network: \n");
showNetwork(newNet);
time(&time_end);
printf("\n exhausted time: %ld \n",time_end-time_begin);
}
void
netToPajek(char * netfile, char * pajekfile)
{
FILE * outfile;
FILE * pFile_pajek;
struct network* target;
// 1) input network and analyze the properties
target=NULL;
outfile=fopen(netfile, "r");
inputNetwork(&target, outfile);
fclose (outfile);
printf("\n %d %d \n", target->nodeNum, target->linkNum);
// 2) to pajek file
pFile_pajek=fopen(pajekfile, "w");
outputNetwork_pajek_frac( target, pFile_pajek);
fclose (pFile_pajek);
freeNetwork(target);
}
void
read_AS_caida()
{
FILE * datafile;
FILE * outfile;
struct network* target;
int id1;
int id2;
double weight;
int error;
int totalNum;
struct netInfo* netinfo;
struct CLSTS* clsts;
FILE * pFile_node;
// 1) read the network data from the raw-data file "AS_oregon2.txt"
target=(struct network *)mem_alloc(sizeof(struct network));
totalNum=11461;
initNetwork(target, totalNum, UN_DIRECT_UN_WEIGHT);
datafile = fopen("./realdata/AS_oregon2.txt", "r");
while(1)
{
error=fscanf(datafile, "%d %d \n", &id1, &id2, &weight);
// use (id1 id2 weight) to construct a network
//printf(" %d (%d , %d) %f \n",error, id1,id2,weight);
//getchar();
if(error==-1)
break;
error=addLinkToNetwork(target, id1, id2, 1.0);
error=addLinkToNetwork(target, id2, id1, 1.0);
}
fclose(datafile);
outfile=fopen("./realdata/AS_oregon2_net.txt", "w");
outputNetwork(target, outfile);
fclose (outfile);
freeNetwork(target);
// 2) analyze the properties
target=NULL;
outfile=fopen("./realdata/AS_oregon2_net.txt", "r");
inputNetwork(&target, outfile);
fclose (outfile);
printf("\n %d %d \n", target->nodeNum, target->linkNum);
// getNetwork Info
netinfo=(struct netInfo*)mem_alloc(sizeof(struct netInfo));
initNetInfo(netinfo, target);
getBasicNetInfo(target, netinfo);
clsts=NULL;
getCLSTS(target,&clsts);
getClstNetInfo(target, clsts, netinfo);
pFile_node=fopen("AS_oregon2_node.txt", "w");
outputNodeInfo(netinfo, pFile_node);
fclose (pFile_node);
// statis info
printf(" %.5f %d %.5f %.5f %d %.5f %.5f %d %.5f %.5f \n",
netinfo->av_k,
netinfo->max_k,
netinfo->av_coef,
netinfo->e_loc,
netinfo->S_size,
netinfo->av_s,
netinfo->S_avspl,
netinfo->S_maxspl,
netinfo->e_glob_active,
netinfo->S_e_glob);
freeNetwork(target);
freeCLSTS(clsts);
freeNetInfo(netinfo);
}
