X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.cpp;h=1417b5a34a6e4ca8a133cc6f2c8ae390ffb81271;hb=a98eb683e17d8e49583bf2d215ab7562a4cdca75;hp=5a2a5ec5c504796869b7f0392e6709e66eb62e9f;hpb=dd173a49e37f6bae73a63c32dd7c98d317bb4a79;p=mothur.git diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp index 5a2a5ec..1417b5a 100644 --- a/unifracweightedcommand.cpp +++ b/unifracweightedcommand.cpp @@ -125,13 +125,10 @@ int UnifracWeightedCommand::execute() { 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... @@ -144,14 +141,7 @@ int UnifracWeightedCommand::execute() { 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; scontrol_pressed) { delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } @@ -208,9 +200,8 @@ int UnifracWeightedCommand::execute() { //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 @@ -241,7 +232,7 @@ int UnifracWeightedCommand::execute() { } - 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(); @@ -250,7 +241,6 @@ int UnifracWeightedCommand::execute() { //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()); } @@ -274,7 +264,7 @@ int UnifracWeightedCommand::execute() { } /**************************************************************************************************/ -int UnifracWeightedCommand::createProcesses(Tree* t, Tree* randT, vector< vector > namesOfGroupCombos, vector& sums, vector< vector >& scores) { +int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector > namesOfGroupCombos, vector& sums, vector< vector >& scores) { try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) int process = 1; @@ -291,35 +281,36 @@ int UnifracWeightedCommand::createProcesses(Tree* t, Tree* randT, vector< vector 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()); } @@ -334,11 +325,12 @@ int UnifracWeightedCommand::createProcesses(Tree* t, Tree* randT, vector< vector } /**************************************************************************************************/ -int UnifracWeightedCommand::driver(Tree* t, Tree* randT, vector< vector > namesOfGroupCombos, int start, int num, vector& sums, vector< vector >& scores) { +int UnifracWeightedCommand::driver(Tree* t, vector< vector > namesOfGroupCombos, int start, int num, vector& sums, vector< vector >& 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 @@ -353,16 +345,17 @@ int UnifracWeightedCommand::driver(Tree* t, Tree* randT, vector< vector 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; } @@ -414,16 +407,16 @@ void UnifracWeightedCommand::printWSummaryFile() { 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++; }