X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parsimonycommand.cpp;h=64d249831ad56f5501dd6dd4d44f17bda35daf78;hp=4529f777358ece0b03a6f53d522a54bd7698ac87;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=847cf1477867e920eddf68e1af64838cfc318386 diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp index 4529f77..64d2498 100644 --- a/parsimonycommand.cpp +++ b/parsimonycommand.cpp @@ -8,43 +8,220 @@ */ #include "parsimonycommand.h" +#include "treereader.h" +//********************************************************************************************************************** +vector ParsimonyCommand::setParameters(){ + try { + CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","parsimony-psummary",false,true,true); parameters.push_back(ptree); + CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname); + CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount); + CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); + CommandParameter prandom("random", "String", "", "", "", "", "","",false,false); parameters.push_back(prandom); + CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ParsimonyCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string ParsimonyCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The parsimony command parameters are tree, group, name, count, random, groups, processors and iters. tree parameter is required unless you have valid current tree file or are using random.\n"; + helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 1 valid group.\n"; + helpString += "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"; + helpString += "The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters).\n"; + helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n"; + helpString += "Example parsimony(random=out, iters=500).\n"; + helpString += "The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony),\n"; + helpString += "and iters is 1000. The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n"; + helpString += "Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "ParsimonyCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +string ParsimonyCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "parsimony") { pattern = "[filename],parsimony"; } + else if (type == "psummary") { pattern = "[filename],psummary"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "ParsimonyCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** +ParsimonyCommand::ParsimonyCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["parsimony"] = tempOutNames; + outputTypes["psummary"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand"); + exit(1); + } +} /***********************************************************/ -ParsimonyCommand::ParsimonyCommand() { +ParsimonyCommand::ParsimonyCommand(string option) { try { - globaldata = GlobalData::getInstance(); + abort = false; calledHelp = false; + Groups.clear(); + + //allow user to run help + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} - //randomtree will tell us if user had their own treefile or if they just want the random distribution - randomtree = globaldata->getRandomTree(); + else { + vector myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + map::iterator it; + + ValidParameters validParameter; - //user has entered their own tree - if (randomtree == "") { - T = globaldata->gTree; - tmap = globaldata->gTreemap; - parsFile = globaldata->getTreeFile() + ".parsimony"; - 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); + //check to make sure all parameters are valid for command + for (it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //initialize outputTypes + vector tempOutNames; + outputTypes["parsimony"] = tempOutNames; + outputTypes["psummary"] = tempOutNames; + + //if the user changes the input directory command factory will send this info to us in the output parameter + string inputDir = validParameter.validFile(parameters, "inputdir", false); + if (inputDir == "not found"){ inputDir = ""; } + else { + string path; + it = parameters.find("tree"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["tree"] = inputDir + it->second; } + } + + it = parameters.find("group"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["group"] = inputDir + it->second; } + } + + it = parameters.find("name"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["name"] = inputDir + it->second; } + } + + it = parameters.find("count"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["count"] = inputDir + it->second; } + } + } + + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; } + + randomtree = validParameter.validFile(parameters, "random", false); if (randomtree == "not found") { randomtree = ""; } + + //are you trying to use parsimony without reading a tree or saying you want random distribution + if (randomtree == "") { + //check for required parameters + treefile = validParameter.validFile(parameters, "tree", true); + if (treefile == "not open") { treefile = ""; abort = true; } + else if (treefile == "not found") { //if there is a current design file, use it + treefile = m->getTreeFile(); + if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setTreeFile(treefile); } + + //check for required parameters + groupfile = validParameter.validFile(parameters, "group", true); + if (groupfile == "not open") { abort = true; } + else if (groupfile == "not found") { groupfile = ""; } + else { m->setGroupFile(groupfile); } + + namefile = validParameter.validFile(parameters, "name", true); + if (namefile == "not open") { namefile = ""; abort = true; } + else if (namefile == "not found") { namefile = ""; } + else { m->setNameFile(namefile); } + + countfile = validParameter.validFile(parameters, "count", true); + if (countfile == "not open") { countfile = ""; abort = true; } + else if (countfile == "not found") { countfile = ""; } + else { m->setCountTableFile(countfile); } + + if ((namefile != "") && (countfile != "")) { + m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true; + } + + if ((groupfile != "") && (countfile != "")) { + m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true; + } + + } + + //if the user changes the output directory command factory will send this info to us in the output parameter + string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; if (randomtree == "") { outputDir += m->hasPath(treefile); } } + + //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 = ""; m->clearGroups(); } + else { + m->splitAtDash(groups, Groups); + m->setGroups(Groups); + } + + itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; } + m->mothurConvert(itersString, iters); + + string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } + m->setProcessors(temp); + m->mothurConvert(temp, processors); + + if (countfile=="") { + if (namefile == "") { + vector files; files.push_back(treefile); + parser.getNameFile(files); + } + } + } - - //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) { - cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function ParsimonyCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ParsimonyCommand class function ParsimonyCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand"); exit(1); } } @@ -52,6 +229,69 @@ ParsimonyCommand::ParsimonyCommand() { int ParsimonyCommand::execute() { try { + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + + //randomtree will tell us if user had their own treefile or if they just want the random distribution + //user has entered their own tree + if (randomtree == "") { + + m->setTreeFile(treefile); + + TreeReader* reader; + if (countfile == "") { reader = new TreeReader(treefile, groupfile, namefile); } + else { reader = new TreeReader(treefile, countfile); } + T = reader->getTrees(); + ct = T[0]->getCountTable(); + delete reader; + + if(outputDir == "") { outputDir += m->hasPath(treefile); } + map variables; + variables["[filename]"] = outputDir + m->getSimpleName(treefile) + "."; + + output = new ColumnFile(getOutputFileName("parsimony",variables), itersString); + outputNames.push_back(getOutputFileName("parsimony",variables)); + outputTypes["parsimony"].push_back(getOutputFileName("parsimony",variables)); + + sumFile = getOutputFileName("psummary",variables); + m->openOutputFile(sumFile, outSum); + outputNames.push_back(sumFile); + outputTypes["psummary"].push_back(sumFile); + }else { //user wants random distribution + getUserInput(); + + if(outputDir == "") { outputDir += m->hasPath(randomtree); } + output = new ColumnFile(outputDir+ m->getSimpleName(randomtree), itersString); + outputNames.push_back(outputDir+ m->getSimpleName(randomtree)); + outputTypes["parsimony"].push_back(outputDir+ m->getSimpleName(randomtree)); + } + + //set users groups to analyze + SharedUtil util; + vector mGroups = m->getGroups(); + vector tGroups = ct->getNamesOfGroups(); + util.setGroups(mGroups, tGroups, allGroups, numGroups, "parsimony"); //sets the groups the user wants to analyze + util.getCombos(groupComb, mGroups, numComp); + m->setGroups(mGroups); + + if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); } + + Parsimony pars; + counter = 0; + + Progress* reading; + reading = new Progress("Comparing to random:", iters); + + if (m->control_pressed) { + delete reading; delete output; + delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; } + if (randomtree == "") { outSum.close(); } + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); + m->clearGroups(); + return 0; + } + + //get pscore for users tree userData.resize(numComp,0); //data = AB, AC, BC, ABC. randomData.resize(numComp,0); //data = AB, AC, BC, ABC. @@ -65,13 +305,23 @@ int ParsimonyCommand::execute() { 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. + userData = pars.getValues(T[i], processors, outputDir); //data = AB, AC, BC, ABC. + if (m->control_pressed) { + delete reading; delete output; + delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; } + if (randomtree == "") { outSum.close(); } + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); + m->clearGroups(); + return 0; + } + + //output scores for each combination for(int k = 0; k < numComp; k++) { + //update uscoreFreq - it = uscoreFreq[k].find(userData[k]); + map::iterator it = uscoreFreq[k].find(userData[k]); if (it == uscoreFreq[k].end()) {//new score uscoreFreq[k][userData[k]] = 1; }else{ uscoreFreq[k][userData[k]]++; } @@ -86,17 +336,29 @@ int ParsimonyCommand::execute() { //get pscores for random trees for (int j = 0; j < iters; j++) { + //create new tree with same num nodes and leaves as users - randT = new Tree(); + randT = new Tree(ct); + //create random relationships between nodes randT->assembleRandomTree(); + //get pscore of random tree - randomData = pars->getValues(randT); + randomData = pars.getValues(randT, processors, outputDir); + if (m->control_pressed) { + delete reading; delete output; delete randT; + if (randomtree == "") { outSum.close(); } + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); + delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; } + m->clearGroups(); + return 0; + } + for(int r = 0; r < numComp; r++) { //add trees pscore to map of scores - it2 = rscoreFreq[r].find(randomData[r]); - if (it2 != rscoreFreq[r].end()) {//already have that score + map::iterator it = rscoreFreq[r].find(randomData[r]); + if (it != rscoreFreq[r].end()) {//already have that score rscoreFreq[r][randomData[r]]++; }else{//first time we have seen this score rscoreFreq[r][randomData[r]] = 1; @@ -106,22 +368,40 @@ int ParsimonyCommand::execute() { validScores[randomData[r]] = randomData[r]; } + //update progress bar + reading->update(j); + delete randT; } + }else { //get pscores for random trees for (int j = 0; j < iters; j++) { + //create new tree with same num nodes and leaves as users - randT = new Tree(); + randT = new Tree(ct); //create random relationships between nodes + randT->assembleRandomTree(); + + if (m->control_pressed) { + delete reading; delete output; delete randT; delete ct; + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; + } + + //get pscore of random tree - randomData = pars->getValues(randT); + randomData = pars.getValues(randT, processors, outputDir); + if (m->control_pressed) { + delete reading; delete output; delete randT; delete ct; + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; + } + for(int r = 0; r < numComp; r++) { //add trees pscore to map of scores - it2 = rscoreFreq[r].find(randomData[r]); - if (it2 != rscoreFreq[r].end()) {//already have that score + map::iterator it = rscoreFreq[r].find(randomData[r]); + if (it != rscoreFreq[r].end()) {//already have that score rscoreFreq[r][randomData[r]]++; }else{//first time we have seen this score rscoreFreq[r][randomData[r]] = 1; @@ -131,17 +411,20 @@ int ParsimonyCommand::execute() { validScores[randomData[r]] = randomData[r]; } + //update progress bar + reading->update(j); + delete randT; } } - + for(int a = 0; a < numComp; a++) { 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++) { + for (map::iterator it = validScores.begin(); it != validScores.end(); it++) { if (randomtree == "") { - it2 = uscoreFreq[a].find(it->first); + map::iterator 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 @@ -150,7 +433,7 @@ int ParsimonyCommand::execute() { } //make rscoreFreq map and rCumul - it2 = rscoreFreq[a].find(it->first); + map::iterator it2 = rscoreFreq[a].find(it->first); //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 @@ -163,26 +446,36 @@ int ParsimonyCommand::execute() { } } + if (m->control_pressed) { + delete reading; delete output; + delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; } + if (randomtree == "") { outSum.close(); } + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); + return 0; + } + + //finish progress bar + reading->finish(); + delete reading; + printParsimonyFile(); if (randomtree == "") { printUSummaryFile(); } + + delete output; delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; } - //reset globaldata's treemap if you just did random distrib - if (randomtree != "") { globaldata->gTreemap = savetmap; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;} - //reset randomTree parameter to "" - globaldata->setRandomTree(""); - //reset groups parameter - globaldata->Groups.clear(); globaldata->setGroups(""); + 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 ParsimonyCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ParsimonyCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ParsimonyCommand", "execute"); exit(1); } } @@ -191,43 +484,40 @@ int ParsimonyCommand::execute() { void ParsimonyCommand::printParsimonyFile() { try { vector data; + vector tags; - //format output - out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); + if (randomtree == "") { + tags.push_back("Score"); tags.push_back("UserFreq"); tags.push_back("UserCumul"); tags.push_back("RandFreq"); tags.push_back("RandCumul"); + }else { + 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++) { + for (map::iterator it = validScores.begin(); it != validScores.end(); it++) { if (randomtree == "") { 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{ 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(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"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ParsimonyCommand class function printParsimonyFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ParsimonyCommand", "printParsimonyFile"); exit(1); } } /***********************************************************/ -void ParsimonyCommand::printUSummaryFile() { +int ParsimonyCommand::printUSummaryFile() { try { //column headers - outSum << "Tree#" << '\t' << "Comb" << '\t' << "ParsScore" << '\t' << '\t' << "ParsSig" << endl; + outSum << "Tree#" << '\t' << "Groups" << '\t' << "ParsScore" << '\t' << "ParsSig" << endl; + m->mothurOut("Tree#\tGroups\tParsScore\tParsSig"); m->mothurOutEndLine(); //format output outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint); @@ -236,19 +526,24 @@ 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 (m->control_pressed) { outSum.close(); return 0; } + if (UScoreSig[a][i] > (1/(float)iters)) { + outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl; + cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl; + m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString(UScoreSig[a][i])); m->mothurOutEndLine(); + }else { + outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl; + cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl; + m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString((1/float(iters)))); m->mothurOutEndLine(); + } } } outSum.close(); + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function printUSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ParsimonyCommand class function printUSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ParsimonyCommand", "printUSummaryFile"); exit(1); } } @@ -258,217 +553,48 @@ void ParsimonyCommand::getUserInput() { try { //create treemap - tmap = new TreeMap(); + ct = new CountTable(); - cout << "Please enter the number of groups you would like to analyze: "; + m->mothurOut("Please enter the number of groups you would like to analyze: "); cin >> numGroups; - + m->mothurOutJustToLog(toString(numGroups)); m->mothurOutEndLine(); + int num, count; count = 1; numEachGroup.resize(numGroups, 0); + set nameMap; + map groupMap; + set gps; + for (int i = 1; i <= numGroups; i++) { - cout << "Please enter the number of sequences in group " << i << ": "; + m->mothurOut("Please enter the number of sequences in group " + toString(i) + ": "); cin >> num; - - //set tmaps seqsPerGroup - tmap->seqsPerGroup[toString(i)] = num; - tmap->namesOfGroups.push_back(toString(i)); + m->mothurOutJustToLog(toString(num)); m->mothurOutEndLine(); + gps.insert(toString(i)); + //set tmaps namesOfSeqs for (int j = 0; j < num; j++) { - tmap->namesOfSeqs.push_back(toString(count)); - tmap->treemap[toString(count)].groupname = toString(i); + groupMap[toString(count)] = toString(i); + nameMap.insert(toString(count)); count++; } } - + ct->createTable(nameMap, groupMap, gps); + //clears buffer so next command doesn't have error string s; getline(cin, s); - //save tmap for later - globaldata->gTreemap = tmap; - + m->Treenames = ct->getNamesOfSeqs(); + m->runParse = false; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function getUserInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ParsimonyCommand class function getUserInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ParsimonyCommand", "getUserInput"); exit(1); } } /***********************************************************/ -void ParsimonyCommand::setGroups() { - try { - string allGroups = ""; - numGroups = 0; - //if the user has not entered specific groups to analyze then do them all - if (globaldata->Groups.size() != 0) { - if (globaldata->Groups[0] != "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) { - cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl; - for (int i = 0; i < tmap->namesOfGroups.size(); i++) { - globaldata->Groups.push_back(tmap->namesOfGroups[i]); - numGroups++; - allGroups += tmap->namesOfGroups[i]; - } - }else { - for (int i = 0; i < globaldata->Groups.size(); i++) { - allGroups += tmap->namesOfGroups[i]; - numGroups++; - } - } - }else{//user has enter "all" and wants the default groups - for (int i = 0; i < tmap->namesOfGroups.size(); i++) { - globaldata->Groups.push_back(tmap->namesOfGroups[i]); - numGroups++; - allGroups += tmap->namesOfGroups[i]; - } - globaldata->setGroups(""); - } - }else { - for (int i = 0; i < tmap->namesOfGroups.size(); i++) { - allGroups += tmap->namesOfGroups[i]; - } - numGroups = 1; - } - - //calculate number of comparsions - numComp = 0; - for (int r=0; rGroups[r]+globaldata->Groups[l]); - numComp++; - } - } - - //ABC - if (numComp != 1) { - groupComb.push_back(allGroups); - numComp++; - } - - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ParsimonyCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - -} -/*****************************************************************/ - -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' << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "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 << 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 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] << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << endl; - }else{ - out << inputBuffer << '\t' << setprecision(6) << data[0] << '\t' << data[1] << '\t' << data[2] << endl; - } - } - else{ - if (randomtree == "") { - out << setprecision(6) << data[0] << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << endl; - }else{ - out << setprecision(6) << data[0] << '\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); - } -} -