userData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC...
randomData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC...
- //create new tree with same num nodes and leaves as users
- randT = new Tree();
-
//get weighted scores for users trees
for (int i = 0; i < T.size(); i++) {
- if (m->control_pressed) { delete randT; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
counter = 0;
rScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC...
userData = weighted->getValues(T[i], processors, outputDir); //userData[0] = weightedscore
- if (m->control_pressed) {
- delete randT;
- if (random) { delete output; }
- outSum.close();
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- return 0;
- }
-
+ if (m->control_pressed) { if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
//save users score
for (int s=0; s<numComp; s++) {
namesOfGroupCombos.push_back(groups);
}
}
-
+
+ lines.clear();
+
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors != 1){
int numPairs = namesOfGroupCombos.size();
if(i == processors - 1){
numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
}
- lines.push_back(new linePair(startPos, numPairsPerProcessor));
+ lines.push_back(linePair(startPos, numPairsPerProcessor));
}
}
#endif
//get scores for random trees
for (int j = 0; j < iters; j++) {
-
+
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
- driver(T[i], randT, namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
+ driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
}else{
- createProcesses(T[i], randT, namesOfGroupCombos, sums, rScores);
+ createProcesses(T[i], namesOfGroupCombos, sums, rScores);
}
#else
- driver(T[i], randT, namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
+ driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
#endif
if (m->control_pressed) { delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
//report progress
m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();
}
-
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
-
+ lines.clear();
+
//find the signifigance of the score for summary file
for (int f = 0; f < numComp; f++) {
//sort random scores
}
- if (m->control_pressed) { delete randT; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
printWSummaryFile();
//clear out users groups
globaldata->Groups.clear();
- delete randT;
if (m->control_pressed) {
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
}
/**************************************************************************************************/
-int UnifracWeightedCommand::createProcesses(Tree* t, Tree* randT, vector< vector<string> > namesOfGroupCombos, vector<double>& sums, vector< vector<double> >& scores) {
+int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, vector<double>& sums, vector< vector<double> >& scores) {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 1;
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- driver(t, randT, namesOfGroupCombos, lines[process]->start, lines[process]->num, sums, scores);
+ driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, sums, scores);
//pass numSeqs to parent
ofstream out;
string tempFile = outputDir + toString(getpid()) + ".weightedcommand.results.temp";
m->openOutputFile(tempFile, out);
- for (int i = lines[process]->start; i < (lines[process]->start + lines[process]->num); i++) { out << scores[i][(scores[i].size()-1)] << '\t'; } out << endl;
+ for (int i = lines[process].start; i < (lines[process].start + lines[process].num); i++) { out << scores[i][(scores[i].size()-1)] << '\t'; } out << endl;
out.close();
exit(0);
}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
- driver(t, randT, namesOfGroupCombos, lines[0]->start, lines[0]->num, sums, scores);
+ driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, sums, scores);
//force parent to wait until all the processes are done
for (int i=0;i<(processors-1);i++) {
int temp = processIDS[i];
wait(&temp);
}
-
+
//get data created by processes
for (int i=0;i<(processors-1);i++) {
+
ifstream in;
string s = outputDir + toString(processIDS[i]) + ".weightedcommand.results.temp";
m->openInputFile(s, in);
double tempScore;
- for (int i = lines[process]->start; i < (lines[process]->start + lines[process]->num); i++) { in >> tempScore; scores[i].push_back(tempScore); }
+ for (int j = lines[(i+1)].start; j < (lines[(i+1)].start + lines[(i+1)].num); j++) { in >> tempScore; scores[j].push_back(tempScore); }
in.close();
remove(s.c_str());
}
}
/**************************************************************************************************/
-int UnifracWeightedCommand::driver(Tree* t, Tree* randT, vector< vector<string> > namesOfGroupCombos, int start, int num, vector<double>& sums, vector< vector<double> >& scores) {
+int UnifracWeightedCommand::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, vector<double>& sums, vector< vector<double> >& scores) {
try {
-
+ Tree* randT = new Tree();
+
for (int h = start; h < (start+num); h++) {
- cout << "doing " << h << endl;
+
if (m->control_pressed) { return 0; }
//initialize weighted score
if (m->control_pressed) { delete randT; return 0; }
-
//get wscore of random tree
EstOutput randomData = weighted->getValues(randT, groupA, groupB, sums);
-
+
if (m->control_pressed) { delete randT; return 0; }
//save scores
scores[h].push_back(randomData[0]);
}
-
+
+ delete randT;
+
return 0;
}
if (WScoreSig[count] > (1/(float)iters)) {
outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
- m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t" + toString(WScoreSig[count])); m->mothurOutEndLine();
+ m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t" + toString(WScoreSig[count]) + "\n");
}else{
outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
- m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" + toString((1/float(iters)))); m->mothurOutEndLine();
+ m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" + toString((1/float(iters))) + "\n");
}
}else{
outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
- m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t0.00"); m->mothurOutEndLine();
+ m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t0.00\n");
}
count++;
}
projects / mothur.git / blobdiff