X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.cpp;h=c7340c7b1704c585b70e2677c0701aaf7edb4e33;hb=9651e8e7172d86707b34af15e95ec60ad4c3c3f9;hp=a527a18d28e8ef8613f39c3ce2d2da6b177f3af5;hpb=fc7cf3aac8fd6106fd725b43baa8ab5ca6f836f8;p=mothur.git diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp index a527a18..c7340c7 100644 --- a/parsimonycommand.cpp +++ b/parsimonycommand.cpp @@ -22,20 +22,21 @@ ParsimonyCommand::ParsimonyCommand() { T = globaldata->gTree; tmap = globaldata->gTreemap; parsFile = globaldata->getTreeFile() + ".parsimony"; - openOutputFile(parsFile, out); + parsFileout = globaldata->getTreeFile() + "temp" + ".parsimony"; sumFile = globaldata->getTreeFile() + ".psummary"; openOutputFile(sumFile, outSum); }else { //user wants random distribution savetmap = globaldata->gTreemap; getUserInput(); - parsFile = randomtree + ".rd_parsimony"; - openOutputFile(parsFile, out); + parsFile = randomtree; + parsFileout = globaldata->getTreeFile() + "temp"; } //set users groups to analyze setGroups(); convert(globaldata->getIters(), iters); //how many random trees to generate pars = new Parsimony(tmap); + counter = 0; } catch(exception& e) { @@ -58,14 +59,12 @@ int ParsimonyCommand::execute() { uscoreFreq.resize(numComp); rCumul.resize(numComp); uCumul.resize(numComp); - validScores.resize(numComp); userTreeScores.resize(numComp); UScoreSig.resize(numComp); if (randomtree == "") { //get pscores for users trees for (int i = 0; i < T.size(); i++) { - cout << "Processing tree " << i+1 << endl; userData = pars->getValues(T[i]); //data = AB, AC, BC, ABC. //output scores for each combination @@ -77,7 +76,7 @@ int ParsimonyCommand::execute() { }else{ uscoreFreq[k][userData[k]]++; } //add users score to valid scores - validScores[k][userData[k]] = userData[k]; + validScores[userData[k]] = userData[k]; //save score for summary file userTreeScores[k].push_back(userData[k]); @@ -103,7 +102,7 @@ int ParsimonyCommand::execute() { } //add randoms score to validscores - validScores[r][randomData[r]] = randomData[r]; + validScores[randomData[r]] = randomData[r]; } delete randT; @@ -128,26 +127,25 @@ int ParsimonyCommand::execute() { } //add randoms score to validscores - validScores[r][randomData[r]] = randomData[r]; + validScores[randomData[r]] = randomData[r]; } delete randT; } } - float rcumul = 0.0000; - float ucumul = 0.0000; - for(int a = 0; a < numComp; a++) { - //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print. - for (it = validScores[a].begin(); it != validScores[a].end(); it++) { + float rcumul = 0.0000; + float ucumul = 0.0000; + //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print. + for (it = validScores.begin(); it != validScores.end(); it++) { if (randomtree == "") { it2 = uscoreFreq[a].find(it->first); //user data has that score if (it2 != uscoreFreq[a].end()) { uscoreFreq[a][it->first] /= T.size(); ucumul+= it2->second; } else { uscoreFreq[a][it->first] = 0.0000; } //no user trees with that score //make uCumul map - uCumul[a][it->first] = ucumul-a; + uCumul[a][it->first] = ucumul; } //make rscoreFreq map and rCumul @@ -155,7 +153,7 @@ int ParsimonyCommand::execute() { //get percentage of random trees with that info if (it2 != rscoreFreq[a].end()) { rscoreFreq[a][it->first] /= iters; rcumul+= it2->second; } else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score - rCumul[a][it->first] = rcumul-a; + rCumul[a][it->first] = rcumul; } //find the signifigance of each user trees score when compared to the random trees and save for printing the summary file @@ -191,28 +189,29 @@ int ParsimonyCommand::execute() { /***********************************************************/ void ParsimonyCommand::printParsimonyFile() { try { - //column headers - if (randomtree == "") { - out << "Comb" << '\t' << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl; - }else { - out << "Comb" << '\t' << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl; - } + vector data; //format output out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); - + for(int a = 0; a < numComp; a++) { + initFile(groupComb[a]); //print each line - for (it = validScores[a].begin(); it != validScores[a].end(); it++) { + for (it = validScores.begin(); it != validScores.end(); it++) { if (randomtree == "") { - out << setprecision(6) << groupComb[a] << '\t' << it->first << '\t' << '\t'<< uscoreFreq[a][it->first] << '\t' << uCumul[a][it->first] << '\t' << rscoreFreq[a][it->first] << '\t' << rCumul[a][it->first] << endl; + data.push_back(it->first); data.push_back(uscoreFreq[a][it->first]); data.push_back(uCumul[a][it->first]); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]); }else{ - out << setprecision(6) << groupComb[a] << '\t' << it->first << '\t' << '\t' << rscoreFreq[a][it->first] << '\t' << rCumul[a][it->first] << endl; + data.push_back(it->first); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]); } + output(data); + data.clear(); } + resetFile(); } - out.close(); + out.close(); + inFile.close(); + remove(parsFileout.c_str()); } catch(exception& e) { cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function printParsimonyFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; @@ -227,7 +226,8 @@ void ParsimonyCommand::printParsimonyFile() { void ParsimonyCommand::printUSummaryFile() { try { //column headers - outSum << "Tree#" << '\t' << "Comb" << '\t' << "ParsScore" << '\t' << '\t' << "ParsSig" << endl; + outSum << "Tree#" << '\t' << "Groups" << '\t' << "ParsScore" << '\t' << "ParsSig" << endl; + cout << "Tree#" << '\t' << "Groups" << '\t' << "ParsScore" << '\t' << "ParsSig" << endl; //format output outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint); @@ -236,8 +236,13 @@ void ParsimonyCommand::printUSummaryFile() { //print each line for (int i = 0; i< T.size(); i++) { for(int a = 0; a < numComp; a++) { - outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << '\t' << UScoreSig[a][i] << endl; - cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << '\t' << UScoreSig[a][i] << endl; + if (UScoreSig[a][i] > (1/(float)iters)) { + outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << UScoreSig[a][i] << endl; + cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << UScoreSig[a][i] << endl; + }else { + outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << "<" << (1/float(iters)) << endl; + cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << "<" << (1/float(iters)) << endl; + } } } @@ -324,26 +329,31 @@ void ParsimonyCommand::setGroups() { for (int i = 0; i < tmap->namesOfGroups.size(); i++) { globaldata->Groups.push_back(tmap->namesOfGroups[i]); numGroups++; - allGroups += tmap->namesOfGroups[i]; + allGroups += tmap->namesOfGroups[i] + "-"; } + allGroups = allGroups.substr(0, allGroups.length()-1); }else { for (int i = 0; i < globaldata->Groups.size(); i++) { - allGroups += tmap->namesOfGroups[i]; + allGroups += globaldata->Groups[i] + "-"; numGroups++; } + allGroups = allGroups.substr(0, allGroups.length()-1); } }else{//user has enter "all" and wants the default groups + globaldata->Groups.clear(); for (int i = 0; i < tmap->namesOfGroups.size(); i++) { globaldata->Groups.push_back(tmap->namesOfGroups[i]); numGroups++; - allGroups += tmap->namesOfGroups[i]; + allGroups += tmap->namesOfGroups[i] + "-"; } + allGroups = allGroups.substr(0, allGroups.length()-1); globaldata->setGroups(""); } }else { for (int i = 0; i < tmap->namesOfGroups.size(); i++) { - allGroups += tmap->namesOfGroups[i]; + allGroups += tmap->namesOfGroups[i] + "-"; } + allGroups = allGroups.substr(0, allGroups.length()-1); numGroups = 1; } @@ -351,7 +361,7 @@ void ParsimonyCommand::setGroups() { numComp = 0; for (int r=0; rGroups[r]+globaldata->Groups[l]); + groupComb.push_back(globaldata->Groups[r]+ "-" +globaldata->Groups[l]); numComp++; } } @@ -375,4 +385,100 @@ void ParsimonyCommand::setGroups() { } /*****************************************************************/ +void ParsimonyCommand::initFile(string label){ + try { + if(counter != 0){ + openOutputFile(parsFileout, out); + openInputFile(parsFile, inFile); + + string inputBuffer; + getline(inFile, inputBuffer); + + if (randomtree == "") { + out << inputBuffer << '\t' << label + "Score" << '\t' << label + "UserFreq" << '\t' << label + "UserCumul" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl; + }else { + out << inputBuffer << '\t' << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl; + } + }else{ + openOutputFile(parsFileout, out); + //column headers + if (randomtree == "") { + out << label + "Score" << '\t' << label + "UserFreq" << '\t' << label + "UserCumul" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl; + }else { + out << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl; + } + } + + out.setf(ios::fixed, ios::floatfield); + out.setf(ios::showpoint); + } + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the ParsimonyCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} + +/***********************************************************************/ + +void ParsimonyCommand::output(vector data){ + try { + if(counter != 0){ + string inputBuffer; + getline(inFile, inputBuffer); + + if (randomtree == "") { + out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << endl; + }else{ + out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << endl; + } + } + else{ + if (randomtree == "") { + out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << endl; + }else{ + out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << endl; + } + } + + } + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the ParsimonyCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} + +/***********************************************************************/ + +void ParsimonyCommand::resetFile(){ + try { + if(counter != 0){ + out.close(); + inFile.close(); + } + else{ + out.close(); + } + counter = 1; + + remove(parsFile.c_str()); + rename(parsFileout.c_str(), parsFile.c_str()); + } + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the ParsimonyCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} +