X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.cpp;h=4ded9c51d399de1bf07950da88e0cb3a19e333d0;hb=794b3f789d6160c99b75edb9cf9af5cf3df4b9da;hp=5f7b4ad5363a2660aa2df7ac9ecb8f3fa998a13d;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d;p=mothur.git diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp index 5f7b4ad..4ded9c5 100644 --- a/unifracweightedcommand.cpp +++ b/unifracweightedcommand.cpp @@ -9,58 +9,204 @@ #include "unifracweightedcommand.h" +//********************************************************************************************************************** +vector UnifracWeightedCommand::getValidParameters(){ + try { + string Array[] = {"groups","iters","distance","random","processors","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "UnifracWeightedCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +UnifracWeightedCommand::UnifracWeightedCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["weighted"] = tempOutNames; + outputTypes["wsummary"] = tempOutNames; + outputTypes["phylip"] = tempOutNames; + outputTypes["column"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector UnifracWeightedCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "UnifracWeightedCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector UnifracWeightedCommand::getRequiredFiles(){ + try { + string Array[] = {"tree","group"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + return myArray; + } + catch(exception& e) { + m->errorOut(e, "UnifracWeightedCommand", "getRequiredFiles"); + exit(1); + } +} /***********************************************************/ -UnifracWeightedCommand::UnifracWeightedCommand() { +UnifracWeightedCommand::UnifracWeightedCommand(string option) { try { globaldata = GlobalData::getInstance(); + abort = false; + Groups.clear(); + + //allow user to run help + if(option == "help") { help(); abort = true; } - T = globaldata->gTree; - tmap = globaldata->gTreemap; - sumFile = globaldata->getTreeFile() + ".wsummary"; - openOutputFile(sumFile, outSum); - - 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(""); + else { + //valid paramters for this command + string Array[] = {"groups","iters","distance","random","processors","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + OptionParser parser(option); + map parameters=parser.getParameters(); + + ValidParameters validParameter; + + //check to make sure all parameters are valid for command + for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //initialize outputTypes + vector tempOutNames; + outputTypes["weighted"] = tempOutNames; + outputTypes["wsummary"] = tempOutNames; + outputTypes["phylip"] = tempOutNames; + outputTypes["column"] = tempOutNames; + + if (globaldata->gTree.size() == 0) {//no trees were read + m->mothurOut("You must execute the read.tree command, before you may execute the unifrac.weighted command."); m->mothurOutEndLine(); abort = true; } + + //if the user changes the output directory command factory will send this info to us in the output parameter + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ + outputDir = ""; + outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it + } + + //check for optional parameter and set defaults + // ...at some point should added some additional type checking... + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { + m->splitAtDash(groups, Groups); + globaldata->Groups = Groups; + } - convert(globaldata->getIters(), iters); //how many random trees to generate - weighted = new Weighted(tmap); + itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; } + convert(itersString, iters); + + string temp = validParameter.validFile(parameters, "distance", false); + if (temp == "not found") { phylip = false; outputForm = ""; } + else{ + if ((temp == "lt") || (temp == "column") || (temp == "square")) { phylip = true; outputForm = temp; } + else { m->mothurOut("Options for distance are: lt, square, or column. Using lt."); m->mothurOutEndLine(); phylip = true; outputForm = "lt"; } + } + + temp = validParameter.validFile(parameters, "random", false); if (temp == "not found") { temp = "F"; } + random = m->isTrue(temp); + + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; } + convert(temp, processors); + + if (!random) { iters = 0; } //turn off random calcs + + if (abort == false) { + T = globaldata->gTree; + tmap = globaldata->gTreemap; + sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".wsummary"; + m->openOutputFile(sumFile, outSum); + outputNames.push_back(sumFile); outputTypes["wsummary"].push_back(sumFile); + + 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); + + weighted = new Weighted(tmap); + + } + } + + } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function UnifracWeightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the UnifracWeightedCommand class function UnifracWeightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +//********************************************************************************************************************** + +void UnifracWeightedCommand::help(){ + try { + m->mothurOut("The unifrac.weighted command can only be executed after a successful read.tree command.\n"); + m->mothurOut("The unifrac.weighted command parameters are groups, iters, distance, processors and random. No parameters are required.\n"); + m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n"); + m->mothurOut("The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n"); + m->mothurOut("The distance parameter allows you to create a distance file from the results. The default is false.\n"); + m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is false, meaning don't compare your trees with randomly generated trees.\n"); + m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n"); + m->mothurOut("The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters).\n"); + m->mothurOut("Example unifrac.weighted(groups=A-B-C, iters=500).\n"); + m->mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n"); + m->mothurOut("The unifrac.weighted command output two files: .weighted and .wsummary their descriptions are in the manual.\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n"); + } + catch(exception& e) { + m->errorOut(e, "UnifracWeightedCommand", "help"); exit(1); } } + /***********************************************************/ int UnifracWeightedCommand::execute() { try { - Progress* reading; - reading = new Progress("Comparing to random:", iters); + + if (abort == true) { return 0; } + + int start = time(NULL); //get weighted for users tree 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) { 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... 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 ThreeColumnFile2(globaldata->getTreeFile() + toString(i+1) + ".weighted"); + + if (random) { + output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted", itersString); + outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted"); + outputTypes["weighted"].push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted"); + } - userData = weighted->getValues(T[i]); //userData[0] = weightedscore + userData = weighted->getValues(T[i], processors, outputDir); //userData[0] = weightedscore + + 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; sgetCopy(T[i]); - - //create a random tree with same topology as T[i], but different labels - randT->assembleRandomUnifracTree(globaldata->Groups[r], globaldata->Groups[l]); - //get wscore of random tree - randomData = weighted->getValues(randT, globaldata->Groups[r], globaldata->Groups[l]); - - //save scores - rScores[count].push_back(randomData[0]); - count++; + if (random) { + + //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3; + vector< vector > namesOfGroupCombos; + for (int a=0; a groups; groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]); + namesOfGroupCombos.push_back(groups); } } - //update progress bar - reading->update(j); - - } + lines.clear(); + + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + if(processors != 1){ + int numPairs = namesOfGroupCombos.size(); + int numPairsPerProcessor = numPairs / processors; + + for (int i = 0; i < processors; i++) { + int startPos = i * numPairsPerProcessor; + if(i == processors - 1){ + numPairsPerProcessor = numPairs - i * numPairsPerProcessor; + } + lines.push_back(linePair(startPos, numPairsPerProcessor)); + } + } + #endif - //removeValidScoresDuplicates(); - //find the signifigance of the score for summary file - for (int f = 0; f < numComp; f++) { - //sort random scores - sort(rScores[f].begin(), rScores[f].end()); - //the index of the score higher than yours is returned - //so if you have 1000 random trees the index returned is 100 - //then there are 900 trees with a score greater then you. - //giving you a signifigance of 0.900 - int index = findIndex(userData[f], f); if (index == -1) { cout << "error in UnifracWeightedCommand" << endl; exit(1); } //error code - - //the signifigance is the number of trees with the users score or higher - WScoreSig.push_back((iters-index)/(float)iters); - } + //get scores for random trees + for (int j = 0; j < iters; j++) { + + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + if(processors == 1){ + driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores); + }else{ + createProcesses(T[i], namesOfGroupCombos, rScores); + } + #else + driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), 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(); + } + lines.clear(); - //out << "Tree# " << i << endl; - calculateFreqsCumuls(); - printWeightedFile(); + //find the signifigance of the score for summary file + for (int f = 0; f < numComp; f++) { + //sort random scores + sort(rScores[f].begin(), rScores[f].end()); + + //the index of the score higher than yours is returned + //so if you have 1000 random trees the index returned is 100 + //then there are 900 trees with a score greater then you. + //giving you a signifigance of 0.900 + int index = findIndex(userData[f], f); if (index == -1) { m->mothurOut("error in UnifracWeightedCommand"); m->mothurOutEndLine(); exit(1); } //error code + + //the signifigance is the number of trees with the users score or higher + WScoreSig.push_back((iters-index)/(float)iters); + } + + //out << "Tree# " << i << endl; + calculateFreqsCumuls(); + printWeightedFile(); + + delete output; - delete output; + } //clear data rScores.clear(); @@ -123,26 +295,140 @@ int UnifracWeightedCommand::execute() { validScores.clear(); } - //finish progress bar - reading->finish(); - delete reading; + + if (m->control_pressed) { outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } printWSummaryFile(); + if (phylip) { createPhylipFile(); } + //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()); } + return 0; + } + + m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run unifrac.weighted."); m->mothurOutEndLine(); + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "UnifracWeightedCommand", "execute"); + exit(1); + } +} +/**************************************************************************************************/ + +int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector > namesOfGroupCombos, vector< vector >& scores) { + try { +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + int process = 1; + int num = 0; + vector processIDS; + + EstOutput results; + + //loop through and create all the processes you want + while (process != processors) { + int pid = fork(); + + if (pid > 0) { + 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, namesOfGroupCombos, lines[process].start, lines[process].num, 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; + out.close(); + + exit(0); + }else { + m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); + for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } + exit(0); + } + } + + driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, 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 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()); + } + + return 0; +#endif + } + catch(exception& e) { + m->errorOut(e, "UnifracWeightedCommand", "createProcesses"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the UnifracWeightedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} + +/**************************************************************************************************/ +int UnifracWeightedCommand::driver(Tree* t, vector< vector > namesOfGroupCombos, int start, int num, vector< vector >& scores) { + try { + Tree* randT = new Tree(); + + for (int h = start; h < (start+num); h++) { + + if (m->control_pressed) { return 0; } + + //initialize weighted score + string groupA = namesOfGroupCombos[h][0]; + string groupB = namesOfGroupCombos[h][1]; + + //copy T[i]'s info. + randT->getCopy(t); + + //create a random tree with same topology as T[i], but different labels + randT->assembleRandomUnifracTree(groupA, groupB); + + if (m->control_pressed) { delete randT; return 0; } + + //get wscore of random tree + EstOutput randomData = weighted->getValues(randT, groupA, groupB); + + if (m->control_pressed) { delete randT; return 0; } + + //save scores + scores[h].push_back(randomData[0]); + } + + delete randT; + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "UnifracWeightedCommand", "driver"); exit(1); } } @@ -156,25 +442,16 @@ void UnifracWeightedCommand::printWeightedFile() { for(int a = 0; a < numComp; a++) { output->initFile(groupComb[a], tags); //print each line - for (it = validScores.begin(); it != validScores.end(); it++) { + for (map::iterator 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->output(data); data.clear(); } 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"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the UnifracWeightedCommand class function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "UnifracWeightedCommand", "printWeightedFile"); exit(1); } } @@ -185,7 +462,7 @@ void UnifracWeightedCommand::printWSummaryFile() { try { //column headers outSum << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" << endl; - cout << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" << endl; + m->mothurOut("Tree#\tGroups\tWScore\tWSig"); m->mothurOutEndLine(); //format output outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint); @@ -194,12 +471,20 @@ void UnifracWeightedCommand::printWSummaryFile() { int count = 0; for (int i = 0; i < T.size(); i++) { for (int j = 0; j < numComp; j++) { - if (WScoreSig[count] > (1/(float)iters)) { - outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(globaldata->getIters().length()) << WScoreSig[count] << endl; - cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(globaldata->getIters().length()) << WScoreSig[count] << endl; + if (random) { + 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]) + "\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))) + "\n"); + } }else{ - outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl; - cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl; + 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\n"); } count++; } @@ -207,15 +492,89 @@ void UnifracWeightedCommand::printWSummaryFile() { outSum.close(); } 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"; + m->errorOut(e, "UnifracWeightedCommand", "printWSummaryFile"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the UnifracWeightedCommand class function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +/***********************************************************/ +void UnifracWeightedCommand::createPhylipFile() { + try { + int count = 0; + //for each tree + for (int i = 0; i < T.size(); i++) { + + string phylipFileName; + if ((outputForm == "lt") || (outputForm == "square")) { + phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted.phylip.dist"; + outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName); + }else { //column + phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted.column.dist"; + outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName); + } + + ofstream out; + m->openOutputFile(phylipFileName, out); + + if ((outputForm == "lt") || (outputForm == "square")) { + //output numSeqs + out << globaldata->Groups.size() << endl; + } + + //make matrix with scores in it + vector< vector > dists; dists.resize(globaldata->Groups.size()); + for (int i = 0; i < globaldata->Groups.size(); i++) { + dists[i].resize(globaldata->Groups.size(), 0.0); + } + + //flip it so you can print it + for (int r=0; rGroups.size(); r++) { + for (int l = r+1; l < globaldata->Groups.size(); l++) { + dists[r][l] = utreeScores[count]; + dists[l][r] = utreeScores[count]; + count++; + } + } + + //output to file + for (int r=0; rGroups.size(); r++) { + //output name + string name = globaldata->Groups[r]; + if (name.length() < 10) { //pad with spaces to make compatible + while (name.length() < 10) { name += " "; } + } + + if (outputForm == "lt") { + out << name << '\t'; + + //output distances + for (int l = 0; l < r; l++) { out << dists[r][l] << '\t'; } + out << endl; + }else if (outputForm == "square") { + out << name << '\t'; + + //output distances + for (int l = 0; l < globaldata->Groups.size(); l++) { out << dists[r][l] << '\t'; } + out << endl; + }else{ + //output distances + for (int l = 0; l < r; l++) { + string otherName = globaldata->Groups[l]; + if (otherName.length() < 10) { //pad with spaces to make compatible + while (otherName.length() < 10) { otherName += " "; } + } + + out << name << '\t' << otherName << dists[r][l] << endl; + } + } + } + out.close(); + } + } + catch(exception& e) { + m->errorOut(e, "UnifracWeightedCommand", "createPhylipFile"); exit(1); } } - /***********************************************************/ int UnifracWeightedCommand::findIndex(float score, int index) { try{ @@ -225,11 +584,7 @@ int UnifracWeightedCommand::findIndex(float score, int index) { return rScores[index].size(); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the UnifracWeightedCommand class function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "UnifracWeightedCommand", "findIndex"); exit(1); } } @@ -249,7 +604,7 @@ void UnifracWeightedCommand::calculateFreqsCumuls() { for (int f = 0; f < numComp; f++) { for (int i = 0; i < rScores[f].size(); i++) { //looks like 0,0,1,1,1,2,4,7... you want to make a map that say rScoreFreq[0] = 2, rScoreFreq[1] = 3... validScores[rScores[f][i]] = rScores[f][i]; - it = rScoreFreq[f].find(rScores[f][i]); + map::iterator it = rScoreFreq[f].find(rScores[f][i]); if (it != rScoreFreq[f].end()) { rScoreFreq[f][rScores[f][i]]++; }else{ @@ -262,9 +617,9 @@ void UnifracWeightedCommand::calculateFreqsCumuls() { for(int a = 0; a < numComp; a++) { float rcumul = 1.0000; //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++) { + for (map::iterator it = validScores.begin(); it != validScores.end(); it++) { //make rscoreFreq map and rCumul - it2 = rScoreFreq[a].find(it->first); + map::iterator it2 = rScoreFreq[a].find(it->first); rCumul[a][it->first] = rcumul; //get percentage of random trees with that info if (it2 != rScoreFreq[a].end()) { rScoreFreq[a][it->first] /= iters; rcumul-= it2->second; } @@ -274,102 +629,13 @@ void UnifracWeightedCommand::calculateFreqsCumuls() { } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function calculateFreqsCums. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the UnifracWeightedCommand class function calculateFreqsCums. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - -} - -/***************************************************************** - -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"; + m->errorOut(e, "UnifracWeightedCommand", "calculateFreqsCums"); 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); - } - - - -} +/***********************************************************/ -*/