heatmapsimcommand.cpp

   1 /*
   2  *  heatmapsimcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 6/8/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "heatmapsimcommand.h"
  11 #include "sharedjabund.h"
  12 #include "sharedsorabund.h"
  13 #include "sharedjclass.h"
  14 #include "sharedsorclass.h"
  15 #include "sharedjest.h"
  16 #include "sharedsorest.h"
  17 #include "sharedthetayc.h"
  18 #include "sharedthetan.h"
  19 #include "sharedmorisitahorn.h"
  20 #include "sharedbraycurtis.h"
  21
  22
  23 //**********************************************************************************************************************
  24 vector<string> HeatMapSimCommand::setParameters(){
  25         try {
  26                 CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);
  27                 CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
  28                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
  29                 CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn);
  30                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  31                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  32                 CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
  33                 CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize);
  34                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  35                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  36
  37                 vector<string> myArray;
  38                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  39                 return myArray;
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "HeatMapSimCommand", "setParameters");
  43                 exit(1);
  44         }
  45 }
  46 //**********************************************************************************************************************
  47 string HeatMapSimCommand::getHelpString(){
  48         try {
  49                 string helpString = "";
  50                 ValidCalculators validCalculator;
  51                 helpString += "The heatmap.sim command parameters are shared, phylip, column, name, groups, calc, fontsize and label.  shared or phylip or column and name are required unless valid current files exist.\n";
  52                 helpString += "There are two ways to use the heatmap.sim command. The first is with the read.otu command. \n";
  53                 helpString += "With the read.otu command you may use the groups, label and calc parameters. \n";
  54                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n";
  55                 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 is also separated by dashes.\n";
  56                 helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
  57                 helpString += "The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n";
  58                 helpString += "Example heatmap.sim(groups=A-B-C, calc=jabund).\n";
  59                 helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
  60                 helpString +=  validCalculator.printCalc("heat");
  61                 helpString += "The default value for calc is jclass-thetayc.\n";
  62                 helpString += "The heatmap.sim command outputs a .svg file for each calculator you choose at each label you specify.\n";
  63                 helpString += "The second way to use the heatmap.sim command is with a distance file representing the distance bewteen your groups. \n";
  64                 helpString += "Using the command this way, the phylip or column parameter are required, and only one may be used.  If you use a column file the name filename is required. \n";
  65                 helpString += "The heatmap.sim command should be in the following format: heatmap.sim(phylip=yourDistanceFile).\n";
  66                 helpString += "Example heatmap.sim(phylip=amazonGroups.dist).\n";
  67                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  68                 return helpString;
  69         }
  70         catch(exception& e) {
  71                 m->errorOut(e, "HeatMapSimCommand", "getHelpString");
  72                 exit(1);
  73         }
  74 }
  75 //**********************************************************************************************************************
  76 HeatMapSimCommand::HeatMapSimCommand(){
  77         try {
  78                 abort = true; calledHelp = true;
  79                 setParameters();
  80                 vector<string> tempOutNames;
  81                 outputTypes["svg"] = tempOutNames;
  82         }
  83         catch(exception& e) {
  84                 m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
  85                 exit(1);
  86         }
  87 }
  88 //**********************************************************************************************************************
  89
  90 HeatMapSimCommand::HeatMapSimCommand(string option)  {
  91         try {
  92                 abort = false; calledHelp = false;
  93                 allLines = 1;
  94
  95                 //allow user to run help
  96                 if(option == "help") {  help(); abort = true; calledHelp = true; }
  97                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  98
  99                 else {
 100                         vector<string> myArray = setParameters();
 101
 102                         OptionParser parser(option);
 103                         map<string,string> parameters = parser.getParameters();
 104
 105                         ValidParameters validParameter;
 106                         map<string,string>::iterator it;
 107
 108                         //check to make sure all parameters are valid for command
 109                         for (it = parameters.begin(); it != parameters.end(); it++) {
 110                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 111                         }
 112
 113                         //initialize outputTypes
 114                         vector<string> tempOutNames;
 115                         outputTypes["svg"] = tempOutNames;
 116
 117                         format = "";
 118
 119                         //if the user changes the input directory command factory will send this info to us in the output parameter
 120                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 121                         if (inputDir == "not found"){   inputDir = "";          }
 122                         else {
 123                                 string path;
 124                                 it = parameters.find("phylip");
 125                                 //user has given a template file
 126                                 if(it != parameters.end()){
 127                                         path = m->hasPath(it->second);
 128                                         //if the user has not given a path then, add inputdir. else leave path alone.
 129                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 130                                 }
 131
 132                                 it = parameters.find("column");
 133                                 //user has given a template file
 134                                 if(it != parameters.end()){
 135                                         path = m->hasPath(it->second);
 136                                         //if the user has not given a path then, add inputdir. else leave path alone.
 137                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
 138                                 }
 139
 140                                 it = parameters.find("name");
 141                                 //user has given a template file
 142                                 if(it != parameters.end()){
 143                                         path = m->hasPath(it->second);
 144                                         //if the user has not given a path then, add inputdir. else leave path alone.
 145                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 146                                 }
 147
 148                                 it = parameters.find("shared");
 149                                 //user has given a template file
 150                                 if(it != parameters.end()){
 151                                         path = m->hasPath(it->second);
 152                                         //if the user has not given a path then, add inputdir. else leave path alone.
 153                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 154                                 }
 155                         }
 156
 157                         //required parameters
 158                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 159                         if (phylipfile == "not open") { abort = true; }
 160                         else if (phylipfile == "not found") { phylipfile = ""; }
 161                         else {  format = "phylip";      inputfile = phylipfile; m-> setPhylipFile(phylipfile); if (outputDir == "") { outputDir += m->hasPath(phylipfile); }  }
 162
 163                         columnfile = validParameter.validFile(parameters, "column", true);
 164                         if (columnfile == "not open") { abort = true; }
 165                         else if (columnfile == "not found") { columnfile = ""; }
 166                         else {  format = "column";      inputfile = columnfile; m->setColumnFile(columnfile); if (outputDir == "") { outputDir += m->hasPath(columnfile); } }
 167
 168                         sharedfile = validParameter.validFile(parameters, "shared", true);
 169                         if (sharedfile == "not open") { abort = true; }
 170                         else if (sharedfile == "not found") { sharedfile = ""; }
 171                         else {  format = "shared";      inputfile = sharedfile; m->setSharedFile(sharedfile); if (outputDir == "") { outputDir += m->hasPath(sharedfile); } }
 172
 173                         namefile = validParameter.validFile(parameters, "name", true);
 174                         if (namefile == "not open") { abort = true; }
 175                         else if (namefile == "not found") { namefile = ""; }
 176                         else { m->setNameFile(namefile); }
 177
 178
 179                         //error checking on files
 180                         if ((sharedfile == "") && ((phylipfile == "") && (columnfile == "")))   {
 181                                 sharedfile = m->getSharedFile();
 182                                 if (sharedfile != "") { format = "shared"; inputfile = sharedfile; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 183                                 else {
 184                                         //is there are current file available for either of these?
 185                                         //give priority to column, then phylip
 186                                         columnfile = m->getColumnFile();
 187                                         if (columnfile != "") {  format = "column"; inputfile = columnfile; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
 188                                         else {
 189                                                 phylipfile = m->getPhylipFile();
 190                                                 if (phylipfile != "") { format = "phylip";  inputfile = phylipfile; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 191                                                 else {
 192                                                         m->mothurOut("No valid current files. You must provide a shared or phylip or column file."); m->mothurOutEndLine();
 193                                                         abort = true;
 194                                                 }
 195                                         }
 196                                 }
 197                         }
 198                         else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When running the heatmap.sim command with a distance file you may not use both the column and the phylip parameters."); m->mothurOutEndLine(); abort = true; }
 199
 200                         if (columnfile != "") {
 201                                 if (namefile == "") {
 202                                         namefile = m->getNameFile();
 203                                         if (namefile != "") {  m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
 204                                         else {
 205                                                 m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine();
 206                                                 abort = true;
 207                                         }
 208                                 }
 209                         }
 210
 211
 212                         //if the user changes the output directory command factory will send this info to us in the output parameter
 213                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 214
 215                         //check for optional parameter and set defaults
 216                         // ...at some point should added some additional type checking...
 217
 218                         label = validParameter.validFile(parameters, "label", false);
 219                         if (label == "not found") { label = ""; }
 220                         else {
 221                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 222                                 else { allLines = 1;  }
 223                         }
 224
 225                         calc = validParameter.validFile(parameters, "calc", false);
 226                         if (calc == "not found") { calc = "jest-thetayc";  }
 227                         else {
 228                                 if (calc == "default")  {  calc = "jest-thetayc";  }
 229                         }
 230                         m->splitAtDash(calc, Estimators);
 231                         if (m->inUsersGroups("citation", Estimators)) {
 232                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 233                                 //remove citation from list of calcs
 234                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 235                         }
 236
 237                         groups = validParameter.validFile(parameters, "groups", false);
 238                         if (groups == "not found") { groups = ""; }
 239                         else {
 240                                 m->splitAtDash(groups, Groups);
 241                                 m->setGroups(Groups);
 242                         }
 243
 244                         string temp = validParameter.validFile(parameters, "fontsize", false);                          if (temp == "not found") { temp = "24"; }
 245                         m->mothurConvert(temp, fontsize);
 246
 247                         if (abort == false) {
 248                                 ValidCalculators validCalculator;
 249
 250                                 int i;
 251                                 for (i=0; i<Estimators.size(); i++) {
 252                                         if (validCalculator.isValidCalculator("heat", Estimators[i]) == true) {
 253                                                 if (Estimators[i] == "jabund") {
 254                                                         heatCalculators.push_back(new JAbund());
 255                                                 }else if (Estimators[i] == "sorabund") {
 256                                                         heatCalculators.push_back(new SorAbund());
 257                                                 }else if (Estimators[i] == "jclass") {
 258                                                         heatCalculators.push_back(new Jclass());
 259                                                 }else if (Estimators[i] == "sorclass") {
 260                                                         heatCalculators.push_back(new SorClass());
 261                                                 }else if (Estimators[i] == "jest") {
 262                                                         heatCalculators.push_back(new Jest());
 263                                                 }else if (Estimators[i] == "sorest") {
 264                                                         heatCalculators.push_back(new SorEst());
 265                                                 }else if (Estimators[i] == "thetayc") {
 266                                                         heatCalculators.push_back(new ThetaYC());
 267                                                 }else if (Estimators[i] == "thetan") {
 268                                                         heatCalculators.push_back(new ThetaN());
 269                                                 }else if (Estimators[i] == "morisitahorn") {
 270                                                         heatCalculators.push_back(new MorHorn());
 271                                                 }else if (Estimators[i] == "braycurtis") {
 272                                                         heatCalculators.push_back(new BrayCurtis());
 273                                                 }
 274                                         }
 275                                 }
 276
 277                         }
 278                 }
 279
 280
 281
 282         }
 283         catch(exception& e) {
 284                 m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
 285                 exit(1);
 286         }
 287 }
 288 //**********************************************************************************************************************
 289
 290 int HeatMapSimCommand::execute(){
 291         try {
 292
 293                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 294
 295                 heatmap = new HeatMapSim(outputDir, inputfile, fontsize);
 296
 297                 if (format == "shared") {
 298                         runCommandShared();
 299                 }else{  runCommandDist();       }
 300
 301                 delete heatmap;
 302
 303                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } outputTypes.clear(); return 0; }
 304
 305                 m->mothurOutEndLine();
 306                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 307                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 308                 m->mothurOutEndLine();
 309
 310                 return 0;
 311         }
 312         catch(exception& e) {
 313                 m->errorOut(e, "HeatMapSimCommand", "execute");
 314                 exit(1);
 315         }
 316 }
 317
 318 //**********************************************************************************************************************
 319 int HeatMapSimCommand::runCommandShared() {
 320         try {
 321                 //if the users entered no valid calculators don't execute command
 322                 if (heatCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; }
 323
 324                 input = new InputData(sharedfile, "sharedfile");
 325                 lookup = input->getSharedRAbundVectors();
 326                 string lastLabel = lookup[0]->getLabel();
 327
 328                 if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); return 0;}
 329
 330                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 331                 set<string> processedLabels;
 332                 set<string> userLabels = labels;
 333
 334                 if (m->control_pressed) {  delete input;  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  m->clearGroups(); return 0; }
 335
 336                 //as long as you are not at the end of the file or done wih the lines you want
 337                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 338
 339                         if (m->control_pressed) { delete input;  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups(); return 0; }
 340
 341                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 342
 343                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 344                                 vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
 345                                 for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }
 346
 347                                 processedLabels.insert(lookup[0]->getLabel());
 348                                 userLabels.erase(lookup[0]->getLabel());
 349                         }
 350
 351                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 352                                 string saveLabel = lookup[0]->getLabel();
 353
 354                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 355                                 lookup = input->getSharedRAbundVectors(lastLabel);
 356
 357                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 358                                 vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
 359                                 for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]);  }
 360
 361                                 processedLabels.insert(lookup[0]->getLabel());
 362                                 userLabels.erase(lookup[0]->getLabel());
 363
 364                                 //restore real lastlabel to save below
 365                                 lookup[0]->setLabel(saveLabel);
 366                         }
 367
 368                         //prevent memory leak
 369
 370                         lastLabel = lookup[0]->getLabel();
 371
 372                         //get next line to process
 373                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 374                         lookup = input->getSharedRAbundVectors();
 375
 376                 }
 377
 378
 379                 if (m->control_pressed) {  delete input;  m->clearGroups();  return 0; }
 380
 381                 //output error messages about any remaining user labels
 382                 set<string>::iterator it;
 383                 bool needToRun = false;
 384                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 385                         m->mothurOut("Your file does not include the label " + *it);
 386                         if (processedLabels.count(lastLabel) != 1) {
 387                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 388                                 needToRun = true;
 389                         }else {
 390                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 391                         }
 392                 }
 393
 394                 if (m->control_pressed) {  delete input;  m->clearGroups(); return 0; }
 395
 396                 //run last label if you need to
 397                 if (needToRun == true)  {
 398                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) { delete lookup[i]; } }
 399                         lookup = input->getSharedRAbundVectors(lastLabel);
 400
 401                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 402                         vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
 403                         for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]);  }
 404
 405                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 406                 }
 407
 408                 if (m->control_pressed) {  delete input;  m->clearGroups(); return 0; }
 409
 410                 //reset groups parameter
 411                 m->clearGroups();
 412
 413                 delete input;
 414
 415                 return 0;
 416         }
 417         catch(exception& e) {
 418                 m->errorOut(e, "HeatMapSimCommand", "runCommandShared");
 419                 exit(1);
 420         }
 421 }
 422 //**********************************************************************************************************************
 423 int HeatMapSimCommand::runCommandDist() {
 424         try {
 425
 426                 vector< vector<double> > matrix;
 427                 vector<string> names;
 428                 ifstream in;
 429
 430                 //read distance file and create distance vector and names vector
 431                 if (format == "phylip") {
 432                         //read phylip file
 433                         m->openInputFile(phylipfile, in);
 434
 435                         string name;
 436                         int numSeqs;
 437                         in >> numSeqs >> name;
 438
 439                         //save name
 440                         names.push_back(name);
 441
 442                         //resize the matrix and fill with zeros
 443                         matrix.resize(numSeqs);
 444                         for(int i = 0; i < numSeqs; i++) {
 445                                 matrix[i].resize(numSeqs, 0.0);
 446                         }
 447
 448                         //determine if matrix is square or lower triangle
 449                         //if it is square read the distances for the first sequence
 450                         char d;
 451                         bool square;
 452                         while((d=in.get()) != EOF){
 453
 454                                 //is d a number meaning its square
 455                                 if(isalnum(d)){
 456                                         square = true;
 457                                         in.putback(d);
 458
 459                                         for(int i=0;i<numSeqs;i++){
 460                                                 in >> matrix[0][i];
 461                                         }
 462                                         break;
 463                                 }
 464
 465                                 //is d a line return meaning its lower triangle
 466                                 if(d == '\n'){
 467                                         square = false;
 468                                         break;
 469                                 }
 470                         }
 471
 472                         //read rest of matrix
 473                         if (square == true) {
 474                                 for(int i=1;i<numSeqs;i++){
 475                                         in >> name;
 476                                         names.push_back(name);
 477
 478                                         if (m->control_pressed) { return 0; }
 479
 480                                         for(int j=0;j<numSeqs;j++) { in >> matrix[i][j];  }
 481                                         m->gobble(in);
 482                                 }
 483                         }else {
 484                                 double dist;
 485                                 for(int i=1;i<numSeqs;i++){
 486                                         in >> name;
 487                                         names.push_back(name);
 488
 489                                         if (m->control_pressed) { return 0; }
 490
 491                                         for(int j=0;j<i;j++){
 492                                                 in >> dist;
 493                                                 matrix[i][j] = dist;  matrix[j][i] = dist;
 494                                         }
 495                                         m->gobble(in);
 496                                 }
 497                         }
 498                         in.close();
 499                 }else {
 500                         //read names file
 501                         NameAssignment* nameMap = new NameAssignment(namefile);
 502                         nameMap->readMap();
 503
 504                         //put names in order in vector
 505                         for (int i = 0; i < nameMap->size(); i++) {
 506                                 names.push_back(nameMap->get(i));
 507                         }
 508
 509                         //resize matrix
 510                         matrix.resize(nameMap->size());
 511                         for (int i = 0; i < nameMap->size(); i++) {
 512                                 matrix[i].resize(nameMap->size(), 0.0);
 513                         }
 514
 515                         //read column file
 516                         string first, second;
 517                         double dist;
 518                         m->openInputFile(columnfile, in);
 519
 520                         while (!in.eof()) {
 521                                 in >> first >> second >> dist; m->gobble(in);
 522
 523                                 if (m->control_pressed) { return 0; }
 524
 525                                 map<string, int>::iterator itA = nameMap->find(first);
 526                                 map<string, int>::iterator itB = nameMap->find(second);
 527
 528                                 if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + first + "' was not found in the names file, please correct\n"); exit(1);  }
 529                                 if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + second + "' was not found in the names file, please correct\n"); exit(1);  }
 530
 531                                 //save distance
 532                                 matrix[itA->second][itB->second] = dist;
 533                                 matrix[itB->second][itA->second] = dist;
 534                         }
 535                         in.close();
 536
 537                         delete nameMap;
 538                 }
 539
 540
 541                 string outputFileName = heatmap->getPic(matrix, names);
 542                 outputNames.push_back(outputFileName); //vector<vector<double>>, vector<string>
 543                 outputTypes["svg"].push_back(outputFileName);
 544
 545                 return 0;
 546         }
 547         catch(exception& e) {
 548                 m->errorOut(e, "HeatMapSimCommand", "runCommandDist");
 549                 exit(1);
 550         }
 551 }
 552 //**********************************************************************************************************************
 553
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