X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.cpp;h=6dfbd710765478d3e7b5c8dc21ab844fa4a6b231;hb=51cf89e90eef8b300c2786eb1560dd89e6e83445;hp=c2584eabfe07975d103c17c6d93e96e2ae1770e2;hpb=2e5ec5cbbd23637ed20da9bdd544d178a3b5d949;p=mothur.git diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp index c2584ea..6dfbd71 100644 --- a/unifracweightedcommand.cpp +++ b/unifracweightedcommand.cpp @@ -19,7 +19,12 @@ UnifracWeightedCommand::UnifracWeightedCommand() { sumFile = globaldata->getTreeFile() + ".wsummary"; openOutputFile(sumFile, outSum); - setGroups(); //sets the groups the user wants to analyze + util = new SharedUtil(); + string s; //to make work with setgroups + util->setGroups(globaldata->Groups, tmap->namesOfGroups, s, numGroups, "weighted"); //sets the groups the user wants to analyze + util->getCombos(groupComb, globaldata->Groups, numComp); + globaldata->setGroups(""); + convert(globaldata->getIters(), iters); //how many random trees to generate weighted = new Weighted(tmap); @@ -51,8 +56,8 @@ int UnifracWeightedCommand::execute() { counter = 0; rScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC... uScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC... - weightedFile = globaldata->getTreeFile() + toString(i+1) + ".weighted"; - weightedFileout = globaldata->getTreeFile() + "temp." + toString(i+1) + ".weighted"; + + output = new ColumnFile(globaldata->getTreeFile() + toString(i+1) + ".weighted"); userData = weighted->getValues(T[i]); //userData[0] = weightedscore @@ -109,6 +114,8 @@ int UnifracWeightedCommand::execute() { calculateFreqsCumuls(); printWeightedFile(); + delete output; + //clear data rScores.clear(); uScores.clear(); @@ -142,22 +149,19 @@ int UnifracWeightedCommand::execute() { void UnifracWeightedCommand::printWeightedFile() { try { vector data; + vector tags; + tags.push_back("Score"); tags.push_back("RandFreq"); tags.push_back("RandCumul"); for(int a = 0; a < numComp; a++) { - initFile(groupComb[a]); + output->initFile(groupComb[a], tags); //print each line for (it = validScores.begin(); it != validScores.end(); it++) { data.push_back(it->first); data.push_back(rScoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]); - output(data); + output->output(data); data.clear(); } - resetFile(); + output->resetFile(); } - - out.close(); - inFile.close(); - remove(weightedFileout.c_str()); - } catch(exception& e) { cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; @@ -224,80 +228,6 @@ int UnifracWeightedCommand::findIndex(float score, int index) { } } -/***********************************************************/ -void UnifracWeightedCommand::setGroups() { - try { - numGroups = 0; - //if the user has not entered specific groups to analyze then do them all - if (globaldata->Groups.size() == 0) { - for (int i=0; i < tmap->getNumGroups(); i++) { - if (tmap->namesOfGroups[i] != "xxx") { - globaldata->Groups.push_back(tmap->namesOfGroups[i]); - numGroups++; - } - } - }else { - if (globaldata->getGroups() != "all") { - //check that groups are valid - for (int i = 0; i < globaldata->Groups.size(); i++) { - if (tmap->isValidGroup(globaldata->Groups[i]) != true) { - cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl; - // erase the invalid group from globaldata->Groups - globaldata->Groups.erase (globaldata->Groups.begin()+i); - } - } - - //if the user only entered invalid groups - if (globaldata->Groups.size() == 0) { - for (int i=0; i < tmap->getNumGroups(); i++) { - if (tmap->namesOfGroups[i] != "xxx") { - globaldata->Groups.push_back(tmap->namesOfGroups[i]); - numGroups++; - } - } - cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl; - }else if (globaldata->Groups.size() == 1) { - cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl; - globaldata->Groups.clear(); - for (int i=0; i < tmap->getNumGroups(); i++) { - if (tmap->namesOfGroups[i] != "xxx") { - globaldata->Groups.push_back(tmap->namesOfGroups[i]); - numGroups++; - } - } - }else { numGroups = globaldata->Groups.size(); } - }else { //users wants all groups - globaldata->Groups.clear(); - globaldata->setGroups(""); - for (int i=0; i < tmap->getNumGroups(); i++) { - if (tmap->namesOfGroups[i] != "xxx") { - globaldata->Groups.push_back(tmap->namesOfGroups[i]); - numGroups++; - } - } - } - } - - //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3; - numComp = 0; - for (int i=0; iGroups[i] + "-" + globaldata->Groups[l]); - } - } - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the UnifracWeightedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } -} - /***********************************************************/ void UnifracWeightedCommand::calculateFreqsCumuls() { @@ -348,85 +278,9 @@ void UnifracWeightedCommand::calculateFreqsCumuls() { } -/*****************************************************************/ - -void UnifracWeightedCommand::initFile(string label){ - try { - if(counter != 0){ - openOutputFile(weightedFileout, out); - openInputFile(weightedFile, inFile); - - string inputBuffer; - getline(inFile, inputBuffer); - - out << inputBuffer << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl; - }else{ - openOutputFile(weightedFileout, out); - out << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl; - } - - out.setf(ios::fixed, ios::floatfield); - out.setf(ios::showpoint); - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the UnifracWeightedCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } -} - -/***********************************************************************/ - -void UnifracWeightedCommand::output(vector data){ - try { - if(counter != 0){ - string inputBuffer; - getline(inFile, inputBuffer); +/***********************************************************/ - out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << 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 UnifracWeightedCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the UnifracWeightedCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } -}; -/***********************************************************************/ -void UnifracWeightedCommand::resetFile(){ - try { - if(counter != 0){ - out.close(); - inFile.close(); - } - else{ - out.close(); - } - counter = 1; - - remove(weightedFile.c_str()); - rename(weightedFileout.c_str(), weightedFile.c_str()); - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the UnifracWeightedCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } -}