}else if (globaldata->Estimators[i] == "eachgap") {
distCalculator = new eachGapDist();
}else if (globaldata->Estimators[i] == "onegap") {
- distCalculator = new oneGapDist(); }
+ distCalculator = new oneGapDist(); }
}
}
}else {
}
}
}
-
+
//reset calc for next command
globaldata->setCalc("");
}
string filename = globaldata->inputFileName;
if(globaldata->getFastaFile() != "") {
- readSeqs = new ReadFasta(filename); }
+ readSeqs = new ReadFasta(filename); }
else if(globaldata->getNexusFile() != "") {
- readSeqs = new ReadNexus(filename); }
+ readSeqs = new ReadNexus(filename); }
else if(globaldata->getClustalFile() != "") {
- readSeqs = new ReadClustal(filename); }
+ readSeqs = new ReadClustal(filename); }
else if(globaldata->getPhylipFile() != "") {
- readSeqs = new ReadPhylip(filename); }
-
+ readSeqs = new ReadPhylip(filename); }
+
readSeqs->read();
seqDB = readSeqs->getDB();
-
+
int numSeqs = seqDB->getNumSeqs();
cutoff += 0.005;
-
+
string distFile = getRootName(globaldata->getFastaFile()) + "dist";
remove(distFile.c_str());
//# if defined (_WIN32)
- //figure out how to implement the fork and wait commands in windows
+ //figure out how to implement the fork and wait commands in windows
// driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
//# endif
- # if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
- driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
- }
- else if(processors == 2){
-
- int pid = fork();
- if(pid > 0){
- driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", cutoff);
- appendFiles((distFile+"tempa"), distFile);
+#if defined (__APPLE__) || (__MACH__)
+ if(processors == 1){
+ driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
+ }
+ else if(processors == 2){
+
+ int pid = fork();
+ if(pid > 0){
+ driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", cutoff);
+ appendFiles((distFile+"tempa"), distFile);
+ remove((distFile + "tempa").c_str());
+ }
+ else{
+ driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", cutoff);
+ appendFiles((distFile+"tempb"), distFile);
+ remove((distFile + "tempb").c_str());
+ }
+ wait(NULL);
+
+ }
+ else if(processors == 3){
+ int pid1 = fork();
+ if(pid1 > 0){
+ int pid2 = fork();
+ if(pid2 > 0){
+ driver(distCalculator, seqDB, 0, sqrt(3) * numSeqs / 3, distFile + "tempa", cutoff);
+ appendFiles(distFile+"tempa", distFile);
remove((distFile + "tempa").c_str());
}
else{
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", cutoff);
- appendFiles((distFile+"tempb"), distFile);
- remove((distFile + "tempb").c_str());
+ driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", cutoff);
+ appendFiles(distFile+"tempb", distFile);
+ remove((distFile + "tempb").c_str());
}
wait(NULL);
-
}
- else if(processors == 3){
- int pid1 = fork();
- if(pid1 > 0){
- int pid2 = fork();
- if(pid2 > 0){
- driver(distCalculator, seqDB, 0, sqrt(3) * numSeqs / 3, distFile + "tempa", cutoff);
- appendFiles(distFile+"tempa", distFile);
- remove((distFile + "tempa").c_str());
- }
- else{
- driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", cutoff);
- appendFiles(distFile+"tempb", distFile);
- remove((distFile + "tempb").c_str());
- }
- wait(NULL);
+ else{
+ driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", cutoff);
+ appendFiles(distFile+"tempc", distFile);
+ remove((distFile + "tempc").c_str());
+ }
+ wait(NULL);
+ }
+ else if(processors == 4){
+ int pid1 = fork();
+ if(pid1 > 0){
+ int pid2 = fork();
+ if(pid2 > 0){
+ driver(distCalculator, seqDB, 0, numSeqs / 2, distFile + "tempa", cutoff);
+ appendFiles(distFile+"tempa", distFile);
+ remove((distFile + "tempa").c_str());
}
else{
- driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", cutoff);
- appendFiles(distFile+"tempc", distFile);
- remove((distFile + "tempc").c_str());
+ driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", cutoff);
+ appendFiles(distFile+"tempb", distFile);
+ remove((distFile + "tempb").c_str());
}
wait(NULL);
}
- else if(processors == 4){
- int pid1 = fork();
- if(pid1 > 0){
- int pid2 = fork();
- if(pid2 > 0){
- driver(distCalculator, seqDB, 0, numSeqs / 2, distFile + "tempa", cutoff);
- appendFiles(distFile+"tempa", distFile);
- remove((distFile + "tempa").c_str());
- }
- else{
- driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", cutoff);
- appendFiles(distFile+"tempb", distFile);
- remove((distFile + "tempb").c_str());
- }
- wait(NULL);
+ else{
+ int pid3 = fork();
+ if(pid3 > 0){
+ driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", cutoff);
+ appendFiles(distFile+"tempc", distFile);
+ remove((distFile + "tempc").c_str());
}
else{
- int pid3 = fork();
- if(pid3 > 0){
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", cutoff);
- appendFiles(distFile+"tempc", distFile);
- remove((distFile + "tempc").c_str());
- }
- else{
- driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", cutoff);
- appendFiles(distFile+"tempd", distFile);
- remove((distFile + "tempd").c_str());
- }
- wait(NULL);
+ driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", cutoff);
+ appendFiles(distFile+"tempd", distFile);
+ remove((distFile + "tempd").c_str());
}
wait(NULL);
}
wait(NULL);
- # else
- driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
- # endif
-
+ }
+ wait(NULL);
+#elif (linux) || (__linux)
+ if(processors == 1){
+ driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
+ }
+ else if(processors == 2){
+
+ int pid = fork();
+ if(pid > 0){
+ driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", cutoff);
+ appendFiles((distFile+"tempa"), distFile);
+ remove((distFile + "tempa").c_str());
+ }
+ else{
+ driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", cutoff);
+ appendFiles((distFile+"tempb"), distFile);
+ remove((distFile + "tempb").c_str());
+ }
+ wait();
+
+ }
+ else if(processors == 3){
+ int pid1 = fork();
+ if(pid1 > 0){
+ int pid2 = fork();
+ if(pid2 > 0){
+ driver(distCalculator, seqDB, 0, sqrt(3) * numSeqs / 3, distFile + "tempa", cutoff);
+ appendFiles(distFile+"tempa", distFile);
+ remove((distFile + "tempa").c_str());
+ }
+ else{
+ driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", cutoff);
+ appendFiles(distFile+"tempb", distFile);
+ remove((distFile + "tempb").c_str());
+ }
+ wait();
+ }
+ else{
+ driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", cutoff);
+ appendFiles(distFile+"tempc", distFile);
+ remove((distFile + "tempc").c_str());
+ }
+ wait();
+ }
+ else if(processors == 4){
+ int pid1 = fork();
+ if(pid1 > 0){
+ int pid2 = fork();
+ if(pid2 > 0){
+ driver(distCalculator, seqDB, 0, numSeqs / 2, distFile + "tempa", cutoff);
+ appendFiles(distFile+"tempa", distFile);
+ remove((distFile + "tempa").c_str());
+ }
+ else{
+ driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", cutoff);
+ appendFiles(distFile+"tempb", distFile);
+ remove((distFile + "tempb").c_str());
+ }
+ wait();
+ }
+ else{
+ int pid3 = fork();
+ if(pid3 > 0){
+ driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", cutoff);
+ appendFiles(distFile+"tempc", distFile);
+ remove((distFile + "tempc").c_str());
+ }
+ else{
+ driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", cutoff);
+ appendFiles(distFile+"tempd", distFile);
+ remove((distFile + "tempd").c_str());
+ }
+ wait();
+ }
+ wait();
+ }
+ wait();
+
+#else
+ driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
+#endif
+
delete distCalculator;
-
+
return 0;
-
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLine, int endLine, string dFileName, float cutoff){
try {
int startTime = time(NULL);
-
+
ofstream distFile(dFileName.c_str(), ios::trunc);
distFile.setf(ios::fixed, ios::showpoint);
distFile << setprecision(4);
-
- for(int i=startLine;i<endLine;i++){
+ for(int i=startLine;i<endLine;i++){
+
for(int j=0;j<i;j++){
distCalculator->calcDist(align->get(i), align->get(j));
double dist = distCalculator->getDist();
-
+
if(dist <= cutoff){
distFile << align->get(i).getName() << ' ' << align->get(j).getName() << ' ' << dist << endl;
}
-
+
}
if(i % 100 == 0){
cout << i << '\t' << time(NULL) - startTime << endl;
}
-
+
}
cout << endLine-1 << '\t' << time(NULL) - startTime << endl;
-
+
return 1;
}
catch(exception& e) {
cout << "An unknown error has occurred in the DistanceCommand class function driver. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
-
+
}
/**************************************************************************************************/
output << line << endl; // Appending back newline char
}
}
-
+
input.close();
output.close();
}
projects / mothur.git / blobdiff