X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=venncommand.cpp;h=98796b3466fcc344b5e4c990015316a5ae2a0582;hp=e305f2203b52a11d0ac809be3f35dfaf578ab1b3;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d diff --git a/venncommand.cpp b/venncommand.cpp index e305f22..98796b3 100644 --- a/venncommand.cpp +++ b/venncommand.cpp @@ -15,167 +15,591 @@ #include "sharedsobscollectsummary.h" #include "sharedchao1.h" #include "sharedace.h" +#include "nseqs.h" +//********************************************************************************************************************** +vector VennCommand::setParameters(){ + try { + CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(plist); + CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(pshared); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pcalc("calc", "String", "", "", "", "", "","",false,false); parameters.push_back(pcalc); + CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund); + CommandParameter pnseqs("nseqs", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pnseqs); + CommandParameter psharedotus("sharedotus", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(psharedotus); + CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize); + CommandParameter ppermute("permute", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ppermute); + 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, "VennCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string VennCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute, sharedotus, fontsize and label. shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n"; + helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups.\n"; + helpString += "The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n"; + helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n"; + helpString += "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n"; + helpString += "Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n"; + helpString += "The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n"; + helpString += "The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n"; + helpString += "The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a shared file.\n"; + helpString += "The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n"; + helpString += "If you have more than 4 groups, the permute parameter will find all possible combos of 4 of your groups and create pictures for them, default=F.\n"; + helpString += "The only estimators available four 4 groups are sharedsobs and sharedchao.\n"; + helpString += "The sharedotus parameter can be used with the sharedsobs calculator to get the names of the OTUs in each section of the venn diagram. Default=t.\n"; + helpString += "The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n"; + helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "VennCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +string VennCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "svg") { pattern = "[filename],svg"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "VennCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** +VennCommand::VennCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["svg"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "VennCommand", "VennCommand"); + exit(1); + } +} //********************************************************************************************************************** -VennCommand::VennCommand(){ +VennCommand::VennCommand(string option) { try { - globaldata = GlobalData::getInstance(); - format = globaldata->getFormat(); - validCalculator = new ValidCalculators(); - util = new SharedUtil(); - - int i; + abort = false; calledHelp = false; + allLines = 1; + + //allow user to run help + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} + else { + vector myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + map::iterator it; + + 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; } + } + + //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("shared"); + //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["shared"] = inputDir + it->second; } + } + + it = parameters.find("list"); + //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["list"] = inputDir + it->second; } + } + } + + //check for required parameters + listfile = validParameter.validFile(parameters, "list", true); + if (listfile == "not open") { listfile = ""; abort = true; } + else if (listfile == "not found") { listfile = ""; } + else { format = "list"; inputfile = listfile; m->setListFile(listfile); } + + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { sharedfile = ""; abort = true; } + else if (sharedfile == "not found") { sharedfile = ""; } + else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); } + + if ((sharedfile == "") && (listfile == "")) { + //is there are current file available for any of these? + //give priority to shared, then list, then rabund, then sabund + //if there is a current shared file, use it + sharedfile = m->getSharedFile(); + if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } + else { + listfile = m->getListFile(); + if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("No valid current files. You must provide a list or shared file."); 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 = m->hasPath(inputfile); } + + //check for optional parameter and set defaults + // ...at some point should added some additional type checking... + label = validParameter.validFile(parameters, "label", false); + if (label == "not found") { label = ""; } + else { + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } + else { allLines = 1; } + } + + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { + m->splitAtDash(groups, Groups); + m->setGroups(Groups); + } + + calc = validParameter.validFile(parameters, "calc", false); + if (calc == "not found") { + if(format == "list") { calc = "sobs"; } + else { calc = "sharedsobs"; } + } + else { + if (calc == "default") { + if(format == "list") { calc = "sobs"; } + else { calc = "sharedsobs"; } + } + } + m->splitAtDash(calc, Estimators); + if (m->inUsersGroups("citation", Estimators)) { + ValidCalculators validCalc; validCalc.printCitations(Estimators); + //remove citation from list of calcs + for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } } + } + + string temp; + temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; } + m->mothurConvert(temp, abund); + + temp = validParameter.validFile(parameters, "nseqs", false); if (temp == "not found"){ temp = "f"; } + nseqs = m->isTrue(temp); + + temp = validParameter.validFile(parameters, "permute", false); if (temp == "not found"){ temp = "f"; } + perm = m->isTrue(temp); + + temp = validParameter.validFile(parameters, "sharedotus", false); if (temp == "not found"){ temp = "t"; } + sharedOtus = m->isTrue(temp); + + temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; } + m->mothurConvert(temp, fontsize); + + } + + } + catch(exception& e) { + m->errorOut(e, "VennCommand", "VennCommand"); + exit(1); + } +} +//********************************************************************************************************************** + +int VennCommand::execute(){ + try { + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + ValidCalculators validCalculator; + if (format == "list") { - for (i=0; iEstimators.size(); i++) { - if (validCalculator->isValidCalculator("vennsingle", globaldata->Estimators[i]) == true) { - if (globaldata->Estimators[i] == "sobs") { + for (int i=0; iEstimators[i] == "chao") { + }else if (Estimators[i] == "chao") { vennCalculators.push_back(new Chao1()); - }else if (globaldata->Estimators[i] == "ace") { - convert(globaldata->getAbund(), abund); - if(abund < 5) - abund = 10; + }else if (Estimators[i] == "ace") { + if(abund < 5) { abund = 10; } vennCalculators.push_back(new Ace(abund)); - //}else if (globaldata->Estimators[i] == "jack") { - //vennCalculators.push_back(new Jackknife()); } } } }else { - for (i=0; iEstimators.size(); i++) { - if (validCalculator->isValidCalculator("vennshared", globaldata->Estimators[i]) == true) { - if (globaldata->Estimators[i] == "sharedsobs") { + for (int i=0; iEstimators[i] == "sharedchao") { + }else if (Estimators[i] == "sharedchao") { vennCalculators.push_back(new SharedChao1()); - }else if (globaldata->Estimators[i] == "sharedace") { + }else if (Estimators[i] == "sharedace") { vennCalculators.push_back(new SharedAce()); } } } } + + //if the users entered no valid calculators don't execute command + if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); return 0; } - venn = new Venn(); - - //reset calc for next command - globaldata->setCalc(""); - - - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the VennCommand class function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } -} -//********************************************************************************************************************** - -VennCommand::~VennCommand(){ - delete input; - delete read; - delete venn; - delete util; -} - -//********************************************************************************************************************** - -int VennCommand::execute(){ - try { - int count = 1; + venn = new Venn(outputDir, nseqs, inputfile, fontsize, sharedOtus); + input = new InputData(inputfile, format); - //if the users entered no valid calculators don't execute command - if (vennCalculators.size() == 0) { return 0; } + string lastLabel; if (format == "sharedfile") { - //you have groups - read = new ReadPhilFile(globaldata->inputFileName); - read->read(&*globaldata); - - input = globaldata->ginput; - order = input->getSharedOrderVector(); - }else if (format == "shared") { - //you are using a list and a groupfile - read = new ReadPhilFile(globaldata->inputFileName); - read->read(&*globaldata); - - input = globaldata->ginput; - SharedList = globaldata->gSharedList; - order = SharedList->getSharedOrderVector(); + lookup = input->getSharedRAbundVectors(); + lastLabel = lookup[0]->getLabel(); + + if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); } }else if (format == "list") { - //you are using just a list file and have only one group - read = new ReadPhilFile(globaldata->inputFileName); - read->read(&*globaldata); - - ordersingle = globaldata->gorder; - input = globaldata->ginput; + sabund = input->getSAbundVector(); + lastLabel = sabund->getLabel(); } - + //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. + set processedLabels; + set userLabels = labels; + if (format != "list") { - util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "venn"); - globaldata->setGroups(""); + //as long as you are not at the end of the file or done wih the lines you want + while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - while(order != NULL){ - - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ - - cout << order->getLabel() << '\t' << count << endl; - venn->getPic(order, vennCalculators); + if (m->control_pressed) { + for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + m->clearGroups(); delete venn; delete input; + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } + return 0; + } + + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + + if ((lookup.size() > 4) && (!perm)){ + m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine(); + for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor + + vector outfilenames = venn->getPic(lookup, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } } + + }else if ((lookup.size() > 4) && (perm)) { + set< set >::iterator it3; + set::iterator it2; + for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) { + + set poss = *it3; + vector subset; + for (it2 = poss.begin(); it2 != poss.end(); it2++) { subset.push_back(lookup[*it2]); } + + vector outfilenames = venn->getPic(subset, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } } + } + }else { + vector outfilenames = venn->getPic(lookup, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } } + } + } + + if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = lookup[0]->getLabel(); + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input->getSharedRAbundVectors(lastLabel); + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + if ((lookup.size() > 4) && (!perm)){ + m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine(); + for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor + + vector outfilenames = venn->getPic(lookup, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } } + + }else if ((lookup.size() > 4) && (perm)) { + set< set >::iterator it3; + set::iterator it2; + for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) { + + set poss = *it3; + vector subset; + for (it2 = poss.begin(); it2 != poss.end(); it2++) { subset.push_back(lookup[*it2]); } + + vector outfilenames = venn->getPic(subset, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } } + } + }else { + vector outfilenames = venn->getPic(lookup, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } } + } + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); } + + + lastLabel = lookup[0]->getLabel(); //get next line to process - if (format == "sharedfile") { - order = input->getSharedOrderVector(); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input->getSharedRAbundVectors(); + } + + if (m->control_pressed) { + for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } + m->clearGroups(); delete venn; delete input; + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } + return 0; + } + + + //output error messages about any remaining user labels + set::iterator it; + bool needToRun = false; + for (it = userLabels.begin(); it != userLabels.end(); it++) { + m->mothurOut("Your file does not include the label " + *it); + if (processedLabels.count(lastLabel) != 1) { + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); + needToRun = true; }else { - //you are using a list and a groupfile - SharedList = input->getSharedListVector(); //get new list vector to process - if (SharedList != NULL) { - order = SharedList->getSharedOrderVector(); //gets new order vector with group info. - }else { - break; - } + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } - count++; } + + //run last label if you need to + if (needToRun == true) { + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } + lookup = input->getSharedRAbundVectors(lastLabel); + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + + if ((lookup.size() > 4) && (!perm)){ + m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine(); + for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor + + vector outfilenames = venn->getPic(lookup, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } } + + }else if ((lookup.size() > 4) && (perm)) { + set< set >::iterator it3; + set::iterator it2; + for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) { + set poss = *it3; + vector subset; + for (it2 = poss.begin(); it2 != poss.end(); it2++) { subset.push_back(lookup[*it2]); } + + vector outfilenames = venn->getPic(subset, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } } + } + }else { + vector outfilenames = venn->getPic(lookup, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } } + } + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + } + + //reset groups parameter - globaldata->Groups.clear(); + m->clearGroups(); + + if (m->control_pressed) { + m->clearGroups(); delete venn; delete input; + for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } + return 0; + } + }else{ - while(ordersingle != NULL){ - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(ordersingle->getLabel()) == 1){ + while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + + if (m->control_pressed) { + for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } + delete sabund; delete venn; delete input; + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } + return 0; + } + + if(allLines == 1 || labels.count(sabund->getLabel()) == 1){ - cout << ordersingle->getLabel() << '\t' << count << endl; - venn->getPic(ordersingle, vennCalculators); + m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); + vector outfilenames = venn->getPic(sabund, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } } + + processedLabels.insert(sabund->getLabel()); + userLabels.erase(sabund->getLabel()); } - ordersingle = (input->getOrderVector()); - count++; + if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = sabund->getLabel(); + + delete sabund; + sabund = input->getSAbundVector(lastLabel); + + m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); + vector outfilenames = venn->getPic(sabund, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } } + + + processedLabels.insert(sabund->getLabel()); + userLabels.erase(sabund->getLabel()); + + //restore real lastlabel to save below + sabund->setLabel(saveLabel); + } + + lastLabel = sabund->getLabel(); + + delete sabund; + sabund = input->getSAbundVector(); + } + + if (m->control_pressed) { + for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } + delete venn; delete input; + return 0; + } + + //output error messages about any remaining user labels + set::iterator it; + bool needToRun = false; + for (it = userLabels.begin(); it != userLabels.end(); it++) { + m->mothurOut("Your file does not include the label " + *it); + if (processedLabels.count(lastLabel) != 1) { + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); + needToRun = true; + }else { + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); + } + } + + //run last label if you need to + if (needToRun == true) { + if (sabund != NULL) { delete sabund; } + sabund = input->getSAbundVector(lastLabel); + + m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); + vector outfilenames = venn->getPic(sabund, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } } + + delete sabund; + + } + + if (m->control_pressed) { + delete venn; delete input; + for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } + return 0; } } + for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } + delete venn; delete input; + + 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 VennCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "VennCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the VennCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +//********************************************************************************************************************** +//returns a vector of sets containing the 4 group combinations +set< set > VennCommand::findCombinations(int lookupSize){ + try { + set< set > combos; + + set possibles; + for (int i = 0; i < lookupSize; i++) { possibles.insert(i); } + + getCombos(possibles, combos); + + return combos; + + } + catch(exception& e) { + m->errorOut(e, "VennCommand", "findCombinations"); exit(1); - } + } } - //********************************************************************************************************************** +//recusively finds combos of 4 +int VennCommand::getCombos(set possibles, set< set >& combos){ + try { + + if (possibles.size() == 4) { //done + if (combos.count(possibles) == 0) { //no dups + combos.insert(possibles); + } + }else { //we still have work to do + set::iterator it; + set::iterator it2; + for (it = possibles.begin(); it != possibles.end(); it++) { + + set newPossibles; + for (it2 = possibles.begin(); it2 != possibles.end(); it2++) { //all possible combos of one length smaller + if (*it != *it2) { + newPossibles.insert(*it2); + } + } + getCombos(newPossibles, combos); + } + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "VennCommand", "getCombos"); + exit(1); + } +} +//**********************************************************************************************************************