X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=heatmapcommand.cpp;h=e07ae220eba02c86117feaa656e2b07015a4b94b;hp=82aa12ce66821443c9cedce4628fad3e43d01674;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp index 82aa12c..e07ae22 100644 --- a/heatmapcommand.cpp +++ b/heatmapcommand.cpp @@ -9,124 +9,546 @@ #include "heatmapcommand.h" - //********************************************************************************************************************** - -HeatMapCommand::HeatMapCommand(){ +vector HeatMapCommand::setParameters(){ try { - globaldata = GlobalData::getInstance(); - heatmap = new HeatMap(); - format = globaldata->getFormat(); - util = new SharedUtil(); + CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(plist); + CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prabund); + CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(psabund); + CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(pshared); + CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prelabund); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); + CommandParameter pscale("scale", "Multiple", "log10-log2-linear", "log10", "", "", "","",false,false); parameters.push_back(pscale); + CommandParameter psorted("sorted", "Multiple", "none-shared-topotu-topgroup", "shared", "", "", "","",false,false); parameters.push_back(psorted); + CommandParameter pnumotu("numotu", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pnumotu); + CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + 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) { - cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "HeatMapCommand", "setParameters"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the HeatMapCommand class function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +//********************************************************************************************************************** +string HeatMapCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The heatmap.bin command parameters are shared, relabund, list, rabund, sabund, groups, sorted, scale, numotu, 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 heatmap.\n"; + helpString += "The sorted parameter allows you to order the otus displayed, default=shared, meaning display the shared otus first. Other options for sorted are none, meaning the exact representation of your otus, \n"; + helpString += "topotu, meaning the otus with the greatest abundance when totaled across groups, topgroup, meaning the top otus for each group. \n"; + helpString += "The scale parameter allows you to choose the range of color your bin information will be displayed with.\n"; + helpString += "The numotu parameter allows you to display only the top N otus, by default all the otus are displayed. You could choose to look at the top 10, by setting numotu=10. The default for sorted is topotu when numotu is used.\n"; + helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like a heatmap 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 heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, label=yourLabels).\n"; + helpString += "Example heatmap.bin(groups=A-B-C, sorted=none, scale=log10).\n"; + helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n"; + helpString += "The default value for scale is log10; your other options are log2 and linear.\n"; + helpString += "The heatmap.bin command outputs a .svg file for each label you specify.\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, "HeatMapCommand", "getHelpString"); exit(1); - } + } } + //********************************************************************************************************************** +string HeatMapCommand::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, "HeatMapCommand", "getOutputPattern"); + exit(1); + } +} -HeatMapCommand::~HeatMapCommand(){ - delete input; - delete read; - delete heatmap; - delete util; +//********************************************************************************************************************** +HeatMapCommand::HeatMapCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["svg"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "HeatMapCommand", "HeatMapCommand"); + exit(1); + } } +//********************************************************************************************************************** + +HeatMapCommand::HeatMapCommand(string option) { + try { + 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 (it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //initialize outputTypes + vector tempOutNames; + outputTypes["svg"] = 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("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("rabund"); + //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["rabund"] = inputDir + it->second; } + } + + it = parameters.find("sabund"); + //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["sabund"] = 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; } + } + + it = parameters.find("relabund"); + //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["relabund"] = inputDir + it->second; } + } + } + + //check for required parameters + listfile = validParameter.validFile(parameters, "list", true); + if (listfile == "not open") { abort = true; } + else if (listfile == "not found") { listfile = ""; } + else { format = "list"; inputfile = listfile; m->setListFile(listfile); } + + sabundfile = validParameter.validFile(parameters, "sabund", true); + if (sabundfile == "not open") { abort = true; } + else if (sabundfile == "not found") { sabundfile = ""; } + else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); } + + rabundfile = validParameter.validFile(parameters, "rabund", true); + if (rabundfile == "not open") { abort = true; } + else if (rabundfile == "not found") { rabundfile = ""; } + else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); } + + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { abort = true; } + else if (sharedfile == "not found") { sharedfile = ""; } + else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); } + + relabundfile = validParameter.validFile(parameters, "relabund", true); + if (relabundfile == "not open") { abort = true; } + else if (relabundfile == "not found") { relabundfile = ""; } + else { format = "relabund"; inputfile = relabundfile; m->setRelAbundFile(relabundfile); } + + + if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "") && (relabundfile == "")) { + //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 { + rabundfile = m->getRabundFile(); + if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); } + else { + sabundfile = m->getSabundFile(); + if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); } + else { + relabundfile = m->getRelAbundFile(); + if (relabundfile != "") { inputfile = relabundfile; format = "relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("No valid current files. You must provide a list, sabund, rabund, relabund 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); + } + + string temp = validParameter.validFile(parameters, "numotu", false); if (temp == "not found") { temp = "0"; } + m->mothurConvert(temp, numOTU); + + temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; } + m->mothurConvert(temp, fontSize); + + sorted = validParameter.validFile(parameters, "sorted", false); + if (sorted == "not found") { + //if numOTU is used change default + if (numOTU != 0) { sorted = "topotu"; } + else { sorted = "shared"; } + } + + scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { scale = "log10"; } + + if ((sorted != "none") && (sorted != "shared") && (sorted != "topotu") && (sorted != "topgroup")) { m->mothurOut(sorted + " is not a valid sorting option. Sorted options are: none, shared, topotu, topgroup"); m->mothurOutEndLine(); abort=true; } + } + } + catch(exception& e) { + m->errorOut(e, "HeatMapCommand", "HeatMapCommand"); + exit(1); + } +} //********************************************************************************************************************** int HeatMapCommand::execute(){ try { - int count = 1; + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir, inputfile); + + string lastLabel; + input = new InputData(inputfile, format); 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(); - }else if (format == "list") { + lookup = input->getSharedRAbundVectors(); + lastLabel = lookup[0]->getLabel(); + + }else if ((format == "list") || (format == "rabund") || (format == "sabund")) { //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; + rabund = input->getRAbundVector(); + lastLabel = rabund->getLabel(); + }else if (format == "relabund") { + //you have groups + lookupFloat = input->getSharedRAbundFloatVectors(); + lastLabel = lookupFloat[0]->getLabel(); } - - if (format != "list") { - - util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "heat"); - globaldata->setGroups(""); - + //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; - while(order != NULL){ + if (format == "sharedfile") { - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ + //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))) { + if (m->control_pressed) { + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear(); + m->clearGroups(); + delete input; delete heatmap; return 0; + } + + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ - cout << order->getLabel() << '\t' << count << endl; - heatmap->getPic(order); - + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + string outputFileName = heatmap->getPic(lookup); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); } - + + 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(); + + string outputFileName = heatmap->getPic(lookup); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); + } + + lastLabel = lookup[0]->getLabel(); + //prevent memory leak + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } + //get next line to process - if (format == "sharedfile") { - order = input->getSharedOrderVector(); + lookup = input->getSharedRAbundVectors(); + } + + + if (m->control_pressed) { + for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear(); + m->clearGroups(); + delete input; delete heatmap; 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(); + string outputFileName = heatmap->getPic(lookup); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + } + //reset groups parameter - globaldata->Groups.clear(); + m->clearGroups(); + + }else if ((format == "list") || (format == "rabund") || (format == "sabund")) { + + while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + if (m->control_pressed) { + for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear(); + delete rabund; delete input; delete heatmap; return 0; + } + + if(allLines == 1 || labels.count(rabund->getLabel()) == 1){ + + m->mothurOut(rabund->getLabel()); m->mothurOutEndLine(); + string outputFileName = heatmap->getPic(rabund); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); + + processedLabels.insert(rabund->getLabel()); + userLabels.erase(rabund->getLabel()); + } + + if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = rabund->getLabel(); + + delete rabund; + rabund = input->getRAbundVector(lastLabel); + m->mothurOut(rabund->getLabel()); m->mothurOutEndLine(); + + string outputFileName = heatmap->getPic(rabund); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); + + processedLabels.insert(rabund->getLabel()); + userLabels.erase(rabund->getLabel()); + + //restore real lastlabel to save below + rabund->setLabel(saveLabel); + } + + + + lastLabel = rabund->getLabel(); + delete rabund; + rabund = input->getRAbundVector(); + } - }else{ - while(ordersingle != NULL){ + if (m->control_pressed) { + for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear(); + delete input; delete heatmap; 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 (rabund != NULL) { delete rabund; } + rabund = input->getRAbundVector(lastLabel); + m->mothurOut(rabund->getLabel()); m->mothurOutEndLine(); + + string outputFileName = heatmap->getPic(rabund); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); + delete rabund; + } + + }else { - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(ordersingle->getLabel()) == 1){ + //as long as you are not at the end of the file or done wih the lines you want + while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + if (m->control_pressed) { + for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } + for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear(); + m->clearGroups(); + delete input; delete heatmap; return 0; + } + + if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){ - cout << ordersingle->getLabel() << '\t' << count << endl; - heatmap->getPic(ordersingle); + m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine(); + string outputFileName = heatmap->getPic(lookupFloat); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); + processedLabels.insert(lookupFloat[0]->getLabel()); + userLabels.erase(lookupFloat[0]->getLabel()); } - ordersingle = (input->getOrderVector()); - count++; + if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = lookupFloat[0]->getLabel(); + + for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } + lookupFloat = input->getSharedRAbundFloatVectors(lastLabel); + m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine(); + + string outputFileName = heatmap->getPic(lookupFloat); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); + + processedLabels.insert(lookupFloat[0]->getLabel()); + userLabels.erase(lookupFloat[0]->getLabel()); + + //restore real lastlabel to save below + lookupFloat[0]->setLabel(saveLabel); + } + + lastLabel = lookupFloat[0]->getLabel(); + //prevent memory leak + for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; lookupFloat[i] = NULL; } + + //get next line to process + lookupFloat = input->getSharedRAbundFloatVectors(); } + + + if (m->control_pressed) { + for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear(); + m->clearGroups(); + delete input; delete heatmap; 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) { + for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } } + lookupFloat = input->getSharedRAbundFloatVectors(lastLabel); + + m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine(); + string outputFileName = heatmap->getPic(lookupFloat); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); + for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } + } + + //reset groups parameter + m->clearGroups(); + } + delete input; + delete heatmap; + + if (m->control_pressed) { + for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear(); return 0; + } + + 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 HeatMapCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "HeatMapCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the HeatMapCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //**********************************************************************************************************************