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
  77 string HeatMapSimCommand::getOutputFileNameTag(string type, string inputName=""){
  78         try {
  79         string outputFileName = "";
  80                 map<string, vector<string> >::iterator it;
  81
  82         //is this a type this command creates
  83         it = outputTypes.find(type);
  84         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  85         else {
  86             if (type == "svg")            {   outputFileName =  "svg";   }
  87             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  88         }
  89         return outputFileName;
  90         }
  91         catch(exception& e) {
  92                 m->errorOut(e, "HeatMapSimCommand", "getOutputFileNameTag");
  93                 exit(1);
  94         }
  95 }
  96
  97 //**********************************************************************************************************************
  98 HeatMapSimCommand::HeatMapSimCommand(){
  99         try {
 100                 abort = true; calledHelp = true;
 101                 setParameters();
 102                 vector<string> tempOutNames;
 103                 outputTypes["svg"] = tempOutNames;
 104         }
 105         catch(exception& e) {
 106                 m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
 107                 exit(1);
 108         }
 109 }
 110 //**********************************************************************************************************************
 111
 112 HeatMapSimCommand::HeatMapSimCommand(string option)  {
 113         try {
 114                 abort = false; calledHelp = false;
 115                 allLines = 1;
 116
 117                 //allow user to run help
 118                 if(option == "help") {  help(); abort = true; calledHelp = true; }
 119                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 120
 121                 else {
 122                         vector<string> myArray = setParameters();
 123
 124                         OptionParser parser(option);
 125                         map<string,string> parameters = parser.getParameters();
 126
 127                         ValidParameters validParameter;
 128                         map<string,string>::iterator it;
 129
 130                         //check to make sure all parameters are valid for command
 131                         for (it = parameters.begin(); it != parameters.end(); it++) {
 132                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 133                         }
 134
 135                         //initialize outputTypes
 136                         vector<string> tempOutNames;
 137                         outputTypes["svg"] = tempOutNames;
 138
 139                         format = "";
 140
 141                         //if the user changes the input directory command factory will send this info to us in the output parameter
 142                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 143                         if (inputDir == "not found"){   inputDir = "";          }
 144                         else {
 145                                 string path;
 146                                 it = parameters.find("phylip");
 147                                 //user has given a template file
 148                                 if(it != parameters.end()){
 149                                         path = m->hasPath(it->second);
 150                                         //if the user has not given a path then, add inputdir. else leave path alone.
 151                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 152                                 }
 153
 154                                 it = parameters.find("column");
 155                                 //user has given a template file
 156                                 if(it != parameters.end()){
 157                                         path = m->hasPath(it->second);
 158                                         //if the user has not given a path then, add inputdir. else leave path alone.
 159                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
 160                                 }
 161
 162                                 it = parameters.find("name");
 163                                 //user has given a template file
 164                                 if(it != parameters.end()){
 165                                         path = m->hasPath(it->second);
 166                                         //if the user has not given a path then, add inputdir. else leave path alone.
 167                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 168                                 }
 169
 170                                 it = parameters.find("shared");
 171                                 //user has given a template file
 172                                 if(it != parameters.end()){
 173                                         path = m->hasPath(it->second);
 174                                         //if the user has not given a path then, add inputdir. else leave path alone.
 175                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 176                                 }
 177                         }
 178
 179                         //required parameters
 180                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 181                         if (phylipfile == "not open") { abort = true; }
 182                         else if (phylipfile == "not found") { phylipfile = ""; }
 183                         else {  format = "phylip";      inputfile = phylipfile; m-> setPhylipFile(phylipfile); if (outputDir == "") { outputDir += m->hasPath(phylipfile); }  }
 184
 185                         columnfile = validParameter.validFile(parameters, "column", true);
 186                         if (columnfile == "not open") { abort = true; }
 187                         else if (columnfile == "not found") { columnfile = ""; }
 188                         else {  format = "column";      inputfile = columnfile; m->setColumnFile(columnfile); if (outputDir == "") { outputDir += m->hasPath(columnfile); } }
 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 = "shared";      inputfile = sharedfile; m->setSharedFile(sharedfile); if (outputDir == "") { outputDir += m->hasPath(sharedfile); } }
 194
 195                         namefile = validParameter.validFile(parameters, "name", true);
 196                         if (namefile == "not open") { abort = true; }
 197                         else if (namefile == "not found") { namefile = ""; }
 198                         else { m->setNameFile(namefile); }
 199
 200
 201                         //error checking on files
 202                         if ((sharedfile == "") && ((phylipfile == "") && (columnfile == "")))   {
 203                                 sharedfile = m->getSharedFile();
 204                                 if (sharedfile != "") { format = "shared"; inputfile = sharedfile; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 205                                 else {
 206                                         //is there are current file available for either of these?
 207                                         //give priority to column, then phylip
 208                                         columnfile = m->getColumnFile();
 209                                         if (columnfile != "") {  format = "column"; inputfile = columnfile; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
 210                                         else {
 211                                                 phylipfile = m->getPhylipFile();
 212                                                 if (phylipfile != "") { format = "phylip";  inputfile = phylipfile; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 213                                                 else {
 214                                                         m->mothurOut("No valid current files. You must provide a shared or phylip or column file."); m->mothurOutEndLine();
 215                                                         abort = true;
 216                                                 }
 217                                         }
 218                                 }
 219                         }
 220                         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; }
 221
 222                         if (columnfile != "") {
 223                                 if (namefile == "") {
 224                                         namefile = m->getNameFile();
 225                                         if (namefile != "") {  m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
 226                                         else {
 227                                                 m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine();
 228                                                 abort = true;
 229                                         }
 230                                 }
 231                         }
 232
 233
 234                         //if the user changes the output directory command factory will send this info to us in the output parameter
 235                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 236
 237                         //check for optional parameter and set defaults
 238                         // ...at some point should added some additional type checking...
 239
 240                         label = validParameter.validFile(parameters, "label", false);
 241                         if (label == "not found") { label = ""; }
 242                         else {
 243                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 244                                 else { allLines = 1;  }
 245                         }
 246
 247                         calc = validParameter.validFile(parameters, "calc", false);
 248                         if (calc == "not found") { calc = "jest-thetayc";  }
 249                         else {
 250                                 if (calc == "default")  {  calc = "jest-thetayc";  }
 251                         }
 252                         m->splitAtDash(calc, Estimators);
 253                         if (m->inUsersGroups("citation", Estimators)) {
 254                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 255                                 //remove citation from list of calcs
 256                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 257                         }
 258
 259                         groups = validParameter.validFile(parameters, "groups", false);
 260                         if (groups == "not found") { groups = ""; }
 261                         else {
 262                                 m->splitAtDash(groups, Groups);
 263                                 m->setGroups(Groups);
 264                         }
 265
 266                         string temp = validParameter.validFile(parameters, "fontsize", false);                          if (temp == "not found") { temp = "24"; }
 267                         m->mothurConvert(temp, fontsize);
 268
 269                         if (abort == false) {
 270                                 ValidCalculators validCalculator;
 271
 272                                 int i;
 273                                 for (i=0; i<Estimators.size(); i++) {
 274                                         if (validCalculator.isValidCalculator("heat", Estimators[i]) == true) {
 275                                                 if (Estimators[i] == "jabund") {
 276                                                         heatCalculators.push_back(new JAbund());
 277                                                 }else if (Estimators[i] == "sorabund") {
 278                                                         heatCalculators.push_back(new SorAbund());
 279                                                 }else if (Estimators[i] == "jclass") {
 280                                                         heatCalculators.push_back(new Jclass());
 281                                                 }else if (Estimators[i] == "sorclass") {
 282                                                         heatCalculators.push_back(new SorClass());
 283                                                 }else if (Estimators[i] == "jest") {
 284                                                         heatCalculators.push_back(new Jest());
 285                                                 }else if (Estimators[i] == "sorest") {
 286                                                         heatCalculators.push_back(new SorEst());
 287                                                 }else if (Estimators[i] == "thetayc") {
 288                                                         heatCalculators.push_back(new ThetaYC());
 289                                                 }else if (Estimators[i] == "thetan") {
 290                                                         heatCalculators.push_back(new ThetaN());
 291                                                 }else if (Estimators[i] == "morisitahorn") {
 292                                                         heatCalculators.push_back(new MorHorn());
 293                                                 }else if (Estimators[i] == "braycurtis") {
 294                                                         heatCalculators.push_back(new BrayCurtis());
 295                                                 }
 296                                         }
 297                                 }
 298
 299                         }
 300                 }
 301
 302
 303
 304         }
 305         catch(exception& e) {
 306                 m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
 307                 exit(1);
 308         }
 309 }
 310 //**********************************************************************************************************************
 311
 312 int HeatMapSimCommand::execute(){
 313         try {
 314
 315                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 316
 317                 heatmap = new HeatMapSim(outputDir, inputfile, fontsize);
 318
 319                 if (format == "shared") {
 320                         runCommandShared();
 321                 }else{  runCommandDist();       }
 322
 323                 delete heatmap;
 324
 325                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } outputTypes.clear(); return 0; }
 326
 327                 m->mothurOutEndLine();
 328                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 329                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 330                 m->mothurOutEndLine();
 331
 332                 return 0;
 333         }
 334         catch(exception& e) {
 335                 m->errorOut(e, "HeatMapSimCommand", "execute");
 336                 exit(1);
 337         }
 338 }
 339
 340 //**********************************************************************************************************************
 341 int HeatMapSimCommand::runCommandShared() {
 342         try {
 343                 //if the users entered no valid calculators don't execute command
 344                 if (heatCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; }
 345
 346                 input = new InputData(sharedfile, "sharedfile");
 347                 lookup = input->getSharedRAbundVectors();
 348                 string lastLabel = lookup[0]->getLabel();
 349
 350                 if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); return 0;}
 351
 352                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 353                 set<string> processedLabels;
 354                 set<string> userLabels = labels;
 355
 356                 if (m->control_pressed) {  delete input;  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  m->clearGroups(); return 0; }
 357
 358                 //as long as you are not at the end of the file or done wih the lines you want
 359                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 360
 361                         if (m->control_pressed) { delete input;  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups(); return 0; }
 362
 363                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 364
 365                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 366                                 vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
 367                                 for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }
 368
 369                                 processedLabels.insert(lookup[0]->getLabel());
 370                                 userLabels.erase(lookup[0]->getLabel());
 371                         }
 372
 373                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 374                                 string saveLabel = lookup[0]->getLabel();
 375
 376                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 377                                 lookup = input->getSharedRAbundVectors(lastLabel);
 378
 379                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 380                                 vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
 381                                 for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]);  }
 382
 383                                 processedLabels.insert(lookup[0]->getLabel());
 384                                 userLabels.erase(lookup[0]->getLabel());
 385
 386                                 //restore real lastlabel to save below
 387                                 lookup[0]->setLabel(saveLabel);
 388                         }
 389
 390                         //prevent memory leak
 391
 392                         lastLabel = lookup[0]->getLabel();
 393
 394                         //get next line to process
 395                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 396                         lookup = input->getSharedRAbundVectors();
 397
 398                 }
 399
 400
 401                 if (m->control_pressed) {  delete input;  m->clearGroups();  return 0; }
 402
 403                 //output error messages about any remaining user labels
 404                 set<string>::iterator it;
 405                 bool needToRun = false;
 406                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 407                         m->mothurOut("Your file does not include the label " + *it);
 408                         if (processedLabels.count(lastLabel) != 1) {
 409                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 410                                 needToRun = true;
 411                         }else {
 412                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 413                         }
 414                 }
 415
 416                 if (m->control_pressed) {  delete input;  m->clearGroups(); return 0; }
 417
 418                 //run last label if you need to
 419                 if (needToRun == true)  {
 420                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) { delete lookup[i]; } }
 421                         lookup = input->getSharedRAbundVectors(lastLabel);
 422
 423                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 424                         vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
 425                         for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]);  }
 426
 427                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 428                 }
 429
 430                 if (m->control_pressed) {  delete input;  m->clearGroups(); return 0; }
 431
 432                 //reset groups parameter
 433                 m->clearGroups();
 434
 435                 delete input;
 436
 437                 return 0;
 438         }
 439         catch(exception& e) {
 440                 m->errorOut(e, "HeatMapSimCommand", "runCommandShared");
 441                 exit(1);
 442         }
 443 }
 444 //**********************************************************************************************************************
 445 int HeatMapSimCommand::runCommandDist() {
 446         try {
 447
 448                 vector< vector<double> > matrix;
 449                 vector<string> names;
 450                 ifstream in;
 451
 452                 //read distance file and create distance vector and names vector
 453                 if (format == "phylip") {
 454                         //read phylip file
 455                         m->openInputFile(phylipfile, in);
 456
 457                         string name;
 458                         int numSeqs;
 459                         in >> numSeqs >> name;
 460
 461                         //save name
 462                         names.push_back(name);
 463
 464                         //resize the matrix and fill with zeros
 465                         matrix.resize(numSeqs);
 466                         for(int i = 0; i < numSeqs; i++) {
 467                                 matrix[i].resize(numSeqs, 0.0);
 468                         }
 469
 470                         //determine if matrix is square or lower triangle
 471                         //if it is square read the distances for the first sequence
 472                         char d;
 473                         bool square;
 474                         while((d=in.get()) != EOF){
 475
 476                                 //is d a number meaning its square
 477                                 if(isalnum(d)){
 478                                         square = true;
 479                                         in.putback(d);
 480
 481                                         for(int i=0;i<numSeqs;i++){
 482                                                 in >> matrix[0][i];
 483                                         }
 484                                         break;
 485                                 }
 486
 487                                 //is d a line return meaning its lower triangle
 488                                 if(d == '\n'){
 489                                         square = false;
 490                                         break;
 491                                 }
 492                         }
 493
 494                         //read rest of matrix
 495                         if (square == true) {
 496                                 for(int i=1;i<numSeqs;i++){
 497                                         in >> name;
 498                                         names.push_back(name);
 499
 500                                         if (m->control_pressed) { return 0; }
 501
 502                                         for(int j=0;j<numSeqs;j++) { in >> matrix[i][j];  }
 503                                         m->gobble(in);
 504                                 }
 505                         }else {
 506                                 double dist;
 507                                 for(int i=1;i<numSeqs;i++){
 508                                         in >> name;
 509                                         names.push_back(name);
 510
 511                                         if (m->control_pressed) { return 0; }
 512
 513                                         for(int j=0;j<i;j++){
 514                                                 in >> dist;
 515                                                 matrix[i][j] = dist;  matrix[j][i] = dist;
 516                                         }
 517                                         m->gobble(in);
 518                                 }
 519                         }
 520                         in.close();
 521                 }else {
 522                         //read names file
 523                         NameAssignment* nameMap = new NameAssignment(namefile);
 524                         nameMap->readMap();
 525
 526                         //put names in order in vector
 527                         for (int i = 0; i < nameMap->size(); i++) {
 528                                 names.push_back(nameMap->get(i));
 529                         }
 530
 531                         //resize matrix
 532                         matrix.resize(nameMap->size());
 533                         for (int i = 0; i < nameMap->size(); i++) {
 534                                 matrix[i].resize(nameMap->size(), 0.0);
 535                         }
 536
 537                         //read column file
 538                         string first, second;
 539                         double dist;
 540                         m->openInputFile(columnfile, in);
 541
 542                         while (!in.eof()) {
 543                                 in >> first >> second >> dist; m->gobble(in);
 544
 545                                 if (m->control_pressed) { return 0; }
 546
 547                                 map<string, int>::iterator itA = nameMap->find(first);
 548                                 map<string, int>::iterator itB = nameMap->find(second);
 549
 550                                 if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + first + "' was not found in the names file, please correct\n"); exit(1);  }
 551                                 if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + second + "' was not found in the names file, please correct\n"); exit(1);  }
 552
 553                                 //save distance
 554                                 matrix[itA->second][itB->second] = dist;
 555                                 matrix[itB->second][itA->second] = dist;
 556                         }
 557                         in.close();
 558
 559                         delete nameMap;
 560                 }
 561
 562
 563                 string outputFileName = heatmap->getPic(matrix, names);
 564                 outputNames.push_back(outputFileName); //vector<vector<double>>, vector<string>
 565                 outputTypes["svg"].push_back(outputFileName);
 566
 567                 return 0;
 568         }
 569         catch(exception& e) {
 570                 m->errorOut(e, "HeatMapSimCommand", "runCommandDist");
 571                 exit(1);
 572         }
 573 }
 574 //**********************************************************************************************************************
 575
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 579
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