heatmapcommand.cpp

   1 /*
   2  *  heatmapcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/25/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "heatmapcommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> HeatMapCommand::setParameters(){
  14         try {
  15                 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
  16                 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
  17                 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
  18                 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
  19                 CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prelabund);
  20                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  21                 CommandParameter pscale("scale", "Multiple", "log10-log2-linear", "log10", "", "", "",false,false); parameters.push_back(pscale);
  22                 CommandParameter psorted("sorted", "Multiple", "none-shared-topotu-topgroup", "shared", "", "", "",false,false); parameters.push_back(psorted);
  23                 CommandParameter pnumotu("numotu", "Number", "", "0", "", "", "",false,false); parameters.push_back(pnumotu);
  24                 CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize);
  25                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  26                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  27                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  28
  29                 vector<string> myArray;
  30                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  31                 return myArray;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "HeatMapCommand", "setParameters");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 string HeatMapCommand::getHelpString(){
  40         try {
  41                 string helpString = "";
  42                 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";
  43                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n";
  44                 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";
  45                 helpString += "topotu, meaning the otus with the greatest abundance when totaled across groups, topgroup, meaning the top otus for each group. \n";
  46                 helpString += "The scale parameter allows you to choose the range of color your bin information will be displayed with.\n";
  47                 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";
  48                 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";
  49                 helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
  50                 helpString += "The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, label=yourLabels).\n";
  51                 helpString += "Example heatmap.bin(groups=A-B-C, sorted=none, scale=log10).\n";
  52                 helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
  53                 helpString += "The default value for scale is log10; your other options are log2 and linear.\n";
  54                 helpString += "The heatmap.bin command outputs a .svg file for each label you specify.\n";
  55                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  56                 return helpString;
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "HeatMapCommand", "getHelpString");
  60                 exit(1);
  61         }
  62 }
  63
  64 //**********************************************************************************************************************
  65
  66 string HeatMapCommand::getOutputFileNameTag(string type, string inputName=""){
  67         try {
  68         string outputFileName = "";
  69                 map<string, vector<string> >::iterator it;
  70
  71         //is this a type this command creates
  72         it = outputTypes.find(type);
  73         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  74         else {
  75             if (type == "svg")            {   outputFileName =  "svg";   }
  76             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  77         }
  78         return outputFileName;
  79         }
  80         catch(exception& e) {
  81                 m->errorOut(e, "HeatMapCommand", "getOutputFileNameTag");
  82                 exit(1);
  83         }
  84 }
  85
  86 //**********************************************************************************************************************
  87 HeatMapCommand::HeatMapCommand(){
  88         try {
  89                 abort = true; calledHelp = true;
  90                 setParameters();
  91                 vector<string> tempOutNames;
  92                 outputTypes["svg"] = tempOutNames;
  93         }
  94         catch(exception& e) {
  95                 m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
  96                 exit(1);
  97         }
  98 }
  99 //**********************************************************************************************************************
 100
 101 HeatMapCommand::HeatMapCommand(string option) {
 102         try {
 103                 abort = false; calledHelp = false;
 104                 allLines = 1;
 105
 106                 //allow user to run help
 107                 if(option == "help") { help(); abort = true; calledHelp = true; }
 108                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 109
 110                 else {
 111                         vector<string> myArray = setParameters();
 112
 113                         OptionParser parser(option);
 114                         map<string,string> parameters = parser.getParameters();
 115                         map<string,string>::iterator it;
 116
 117                         ValidParameters validParameter;
 118
 119                         //check to make sure all parameters are valid for command
 120                         for (it = parameters.begin(); it != parameters.end(); it++) {
 121                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 122                         }
 123
 124                         //initialize outputTypes
 125                         vector<string> tempOutNames;
 126                         outputTypes["svg"] = tempOutNames;
 127
 128                         //if the user changes the input directory command factory will send this info to us in the output parameter
 129                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 130                         if (inputDir == "not found"){   inputDir = "";          }
 131                         else {
 132                                 string path;
 133                                 it = parameters.find("shared");
 134                                 //user has given a template file
 135                                 if(it != parameters.end()){
 136                                         path = m->hasPath(it->second);
 137                                         //if the user has not given a path then, add inputdir. else leave path alone.
 138                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 139                                 }
 140
 141                                 it = parameters.find("rabund");
 142                                 //user has given a template file
 143                                 if(it != parameters.end()){
 144                                         path = m->hasPath(it->second);
 145                                         //if the user has not given a path then, add inputdir. else leave path alone.
 146                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 147                                 }
 148
 149                                 it = parameters.find("sabund");
 150                                 //user has given a template file
 151                                 if(it != parameters.end()){
 152                                         path = m->hasPath(it->second);
 153                                         //if the user has not given a path then, add inputdir. else leave path alone.
 154                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 155                                 }
 156
 157                                 it = parameters.find("list");
 158                                 //user has given a template file
 159                                 if(it != parameters.end()){
 160                                         path = m->hasPath(it->second);
 161                                         //if the user has not given a path then, add inputdir. else leave path alone.
 162                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 163                                 }
 164
 165                                 it = parameters.find("relabund");
 166                                 //user has given a template file
 167                                 if(it != parameters.end()){
 168                                         path = m->hasPath(it->second);
 169                                         //if the user has not given a path then, add inputdir. else leave path alone.
 170                                         if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
 171                                 }
 172                         }
 173
 174                         //check for required parameters
 175                         listfile = validParameter.validFile(parameters, "list", true);
 176                         if (listfile == "not open") { abort = true; }
 177                         else if (listfile == "not found") { listfile = ""; }
 178                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 179
 180                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 181                         if (sabundfile == "not open") {  abort = true; }
 182                         else if (sabundfile == "not found") { sabundfile = ""; }
 183                         else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 184
 185                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 186                         if (rabundfile == "not open") {  abort = true; }
 187                         else if (rabundfile == "not found") { rabundfile = ""; }
 188                         else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 189
 190                         sharedfile = validParameter.validFile(parameters, "shared", true);
 191                         if (sharedfile == "not open") { abort = true; }
 192                         else if (sharedfile == "not found") { sharedfile = ""; }
 193                         else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 194
 195                         relabundfile = validParameter.validFile(parameters, "relabund", true);
 196                         if (relabundfile == "not open") {  abort = true; }
 197                         else if (relabundfile == "not found") { relabundfile = ""; }
 198                         else {  format = "relabund"; inputfile = relabundfile; m->setRelAbundFile(relabundfile); }
 199
 200
 201                         if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "") && (relabundfile == "")) {
 202                                 //is there are current file available for any of these?
 203                                 //give priority to shared, then list, then rabund, then sabund
 204                                 //if there is a current shared file, use it
 205                                 sharedfile = m->getSharedFile();
 206                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 207                                 else {
 208                                         listfile = m->getListFile();
 209                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 210                                         else {
 211                                                 rabundfile = m->getRabundFile();
 212                                                 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 213                                                 else {
 214                                                         sabundfile = m->getSabundFile();
 215                                                         if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 216                                                         else {
 217                                                                 relabundfile = m->getRelAbundFile();
 218                                                                 if (relabundfile != "") { inputfile = relabundfile; format = "relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
 219                                                                 else {
 220                                                                         m->mothurOut("No valid current files. You must provide a list, sabund, rabund, relabund or shared file."); m->mothurOutEndLine();
 221                                                                         abort = true;
 222                                                                 }
 223                                                         }
 224                                                 }
 225                                         }
 226                                 }
 227                         }
 228
 229
 230                         //if the user changes the output directory command factory will send this info to us in the output parameter
 231                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 232
 233                         //check for optional parameter and set defaults
 234                         // ...at some point should added some additional type checking...
 235                         label = validParameter.validFile(parameters, "label", false);
 236                         if (label == "not found") { label = ""; }
 237                         else {
 238                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 239                                 else { allLines = 1;  }
 240                         }
 241
 242
 243                         groups = validParameter.validFile(parameters, "groups", false);
 244                         if (groups == "not found") { groups = ""; }
 245                         else {
 246                                 m->splitAtDash(groups, Groups);
 247                                 m->setGroups(Groups);
 248                         }
 249
 250                         string temp = validParameter.validFile(parameters, "numotu", false);            if (temp == "not found") { temp = "0"; }
 251                         m->mothurConvert(temp, numOTU);
 252
 253                         temp = validParameter.validFile(parameters, "fontsize", false);                         if (temp == "not found") { temp = "24"; }
 254                         m->mothurConvert(temp, fontSize);
 255
 256                         sorted = validParameter.validFile(parameters, "sorted", false);
 257                         if (sorted == "not found") {
 258                                 //if numOTU is used change default
 259                                 if (numOTU != 0) { sorted = "topotu"; }
 260                                 else { sorted = "shared"; }
 261                         }
 262
 263                         scale = validParameter.validFile(parameters, "scale", false);                           if (scale == "not found") { scale = "log10"; }
 264
 265                         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;  }
 266                 }
 267
 268         }
 269         catch(exception& e) {
 270                 m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
 271                 exit(1);
 272         }
 273 }
 274 //**********************************************************************************************************************
 275
 276 int HeatMapCommand::execute(){
 277         try {
 278
 279                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 280
 281                 heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir, inputfile);
 282
 283                 string lastLabel;
 284                 input = new InputData(inputfile, format);
 285
 286                 if (format == "sharedfile") {
 287                         //you have groups
 288                         lookup = input->getSharedRAbundVectors();
 289                         lastLabel = lookup[0]->getLabel();
 290
 291                 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
 292                         //you are using just a list file and have only one group
 293                         rabund = input->getRAbundVector();
 294                         lastLabel = rabund->getLabel();
 295                 }else if (format == "relabund") {
 296                         //you have groups
 297                         lookupFloat = input->getSharedRAbundFloatVectors();
 298                         lastLabel = lookupFloat[0]->getLabel();
 299                 }
 300
 301                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 302                 set<string> processedLabels;
 303                 set<string> userLabels = labels;
 304
 305                 if (format == "sharedfile") {
 306
 307                         //as long as you are not at the end of the file or done wih the lines you want
 308                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 309                                 if (m->control_pressed) {
 310                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 311                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 312                                         m->clearGroups();
 313                                         delete input; delete heatmap; return 0;
 314                                 }
 315
 316                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 317
 318                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 319                                         string outputFileName = heatmap->getPic(lookup);
 320                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 321
 322                                         processedLabels.insert(lookup[0]->getLabel());
 323                                         userLabels.erase(lookup[0]->getLabel());
 324                                 }
 325
 326                                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 327                                         string saveLabel = lookup[0]->getLabel();
 328
 329                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 330
 331                                         lookup = input->getSharedRAbundVectors(lastLabel);
 332                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 333
 334                                         string outputFileName = heatmap->getPic(lookup);
 335                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 336
 337                                         processedLabels.insert(lookup[0]->getLabel());
 338                                         userLabels.erase(lookup[0]->getLabel());
 339
 340                                         //restore real lastlabel to save below
 341                                         lookup[0]->setLabel(saveLabel);
 342                                 }
 343
 344                                 lastLabel = lookup[0]->getLabel();
 345                                 //prevent memory leak
 346                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 347
 348                                 //get next line to process
 349                                 lookup = input->getSharedRAbundVectors();
 350                         }
 351
 352
 353                         if (m->control_pressed) {
 354                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 355                                 m->clearGroups();
 356                                 delete input; delete heatmap; return 0;
 357                         }
 358
 359                         //output error messages about any remaining user labels
 360                         set<string>::iterator it;
 361                         bool needToRun = false;
 362                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 363                                 m->mothurOut("Your file does not include the label " + *it);
 364                                 if (processedLabels.count(lastLabel) != 1) {
 365                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 366                                         needToRun = true;
 367                                 }else {
 368                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 369                                 }
 370                         }
 371
 372                         //run last label if you need to
 373                         if (needToRun == true)  {
 374                                 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 375                                 lookup = input->getSharedRAbundVectors(lastLabel);
 376
 377                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 378                                 string outputFileName = heatmap->getPic(lookup);
 379                                 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 380                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 381                         }
 382
 383                         //reset groups parameter
 384                         m->clearGroups();
 385
 386                 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
 387
 388                         while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 389                                 if (m->control_pressed) {
 390                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 391                                         delete rabund;  delete input; delete heatmap; return 0;
 392                                 }
 393
 394                                 if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
 395
 396                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 397                                         string outputFileName = heatmap->getPic(rabund);
 398                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 399
 400                                         processedLabels.insert(rabund->getLabel());
 401                                         userLabels.erase(rabund->getLabel());
 402                                 }
 403
 404                                 if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 405                                         string saveLabel = rabund->getLabel();
 406
 407                                         delete rabund;
 408                                         rabund = input->getRAbundVector(lastLabel);
 409                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 410
 411                                         string outputFileName = heatmap->getPic(rabund);
 412                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 413
 414                                         processedLabels.insert(rabund->getLabel());
 415                                         userLabels.erase(rabund->getLabel());
 416
 417                                         //restore real lastlabel to save below
 418                                         rabund->setLabel(saveLabel);
 419                                 }
 420
 421
 422
 423                                 lastLabel = rabund->getLabel();
 424                                 delete rabund;
 425                                 rabund = input->getRAbundVector();
 426                         }
 427
 428                         if (m->control_pressed) {
 429                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 430                                 delete input; delete heatmap; return 0;
 431                         }
 432
 433                         //output error messages about any remaining user labels
 434                         set<string>::iterator it;
 435                         bool needToRun = false;
 436                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 437                                 m->mothurOut("Your file does not include the label " + *it);
 438                                 if (processedLabels.count(lastLabel) != 1) {
 439                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 440                                         needToRun = true;
 441                                 }else {
 442                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 443                                 }
 444                         }
 445
 446                         //run last label if you need to
 447                         if (needToRun == true)  {
 448
 449                                 if (rabund != NULL) {   delete rabund;  }
 450                                 rabund = input->getRAbundVector(lastLabel);
 451                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 452
 453                                 string outputFileName = heatmap->getPic(rabund);
 454                                 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 455                                 delete rabund;
 456                         }
 457
 458                 }else {
 459
 460                         //as long as you are not at the end of the file or done wih the lines you want
 461                         while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 462                                 if (m->control_pressed) {
 463                                         for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 464                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 465                                         m->clearGroups();
 466                                         delete input; delete heatmap; return 0;
 467                                 }
 468
 469                                 if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){
 470
 471                                         m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
 472                                         string outputFileName = heatmap->getPic(lookupFloat);
 473                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 474
 475                                         processedLabels.insert(lookupFloat[0]->getLabel());
 476                                         userLabels.erase(lookupFloat[0]->getLabel());
 477                                 }
 478
 479                                 if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 480                                         string saveLabel = lookupFloat[0]->getLabel();
 481
 482                                         for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 483                                         lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 484                                         m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
 485
 486                                         string outputFileName = heatmap->getPic(lookupFloat);
 487                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 488
 489                                         processedLabels.insert(lookupFloat[0]->getLabel());
 490                                         userLabels.erase(lookupFloat[0]->getLabel());
 491
 492                                         //restore real lastlabel to save below
 493                                         lookupFloat[0]->setLabel(saveLabel);
 494                                 }
 495
 496                                 lastLabel = lookupFloat[0]->getLabel();
 497                                 //prevent memory leak
 498                                 for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i]; lookupFloat[i] = NULL; }
 499
 500                                 //get next line to process
 501                                 lookupFloat = input->getSharedRAbundFloatVectors();
 502                         }
 503
 504
 505                         if (m->control_pressed) {
 506                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 507                                 m->clearGroups();
 508                                 delete input; delete heatmap; return 0;
 509                         }
 510
 511                         //output error messages about any remaining user labels
 512                         set<string>::iterator it;
 513                         bool needToRun = false;
 514                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 515                                 m->mothurOut("Your file does not include the label " + *it);
 516                                 if (processedLabels.count(lastLabel) != 1) {
 517                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 518                                         needToRun = true;
 519                                 }else {
 520                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 521                                 }
 522                         }
 523
 524                         //run last label if you need to
 525                         if (needToRun == true)  {
 526                                 for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } }
 527                                 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 528
 529                                 m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
 530                                 string outputFileName = heatmap->getPic(lookupFloat);
 531                                 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 532                                 for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 533                         }
 534
 535                         //reset groups parameter
 536                         m->clearGroups();
 537
 538                 }
 539
 540                 delete input;
 541                 delete heatmap;
 542
 543                 if (m->control_pressed) {
 544                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear(); return 0;
 545                 }
 546
 547                 m->mothurOutEndLine();
 548                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 549                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 550                 m->mothurOutEndLine();
 551
 552                 return 0;
 553         }
 554         catch(exception& e) {
 555                 m->errorOut(e, "HeatMapCommand", "execute");
 556                 exit(1);
 557         }
 558 }
 559
 560 //**********************************************************************************************************************
 561
 562