matrixoutputcommand.cpp

   1 /*
   2  *  matrixoutputcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 5/20/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "matrixoutputcommand.h"
  11 #include "sharedsobscollectsummary.h"
  12 #include "sharedchao1.h"
  13 #include "sharedace.h"
  14 #include "sharednseqs.h"
  15 #include "sharedjabund.h"
  16 #include "sharedsorabund.h"
  17 #include "sharedjclass.h"
  18 #include "sharedsorclass.h"
  19 #include "sharedjest.h"
  20 #include "sharedsorest.h"
  21 #include "sharedthetayc.h"
  22 #include "sharedthetan.h"
  23 #include "sharedkstest.h"
  24 #include "whittaker.h"
  25 #include "sharedochiai.h"
  26 #include "sharedanderbergs.h"
  27 #include "sharedkulczynski.h"
  28 #include "sharedkulczynskicody.h"
  29 #include "sharedlennon.h"
  30 #include "sharedmorisitahorn.h"
  31 #include "sharedbraycurtis.h"
  32 #include "sharedjackknife.h"
  33 #include "whittaker.h"
  34 #include "odum.h"
  35 #include "canberra.h"
  36 #include "structeuclidean.h"
  37 #include "structchord.h"
  38 #include "hellinger.h"
  39 #include "manhattan.h"
  40 #include "structpearson.h"
  41 #include "soergel.h"
  42 #include "spearman.h"
  43 #include "structkulczynski.h"
  44 #include "structchi2.h"
  45 #include "speciesprofile.h"
  46 #include "hamming.h"
  47 #include "gower.h"
  48 #include "memchi2.h"
  49 #include "memchord.h"
  50 #include "memeuclidean.h"
  51 #include "mempearson.h"
  52
  53 //**********************************************************************************************************************
  54 vector<string> MatrixOutputCommand::setParameters(){
  55         try {
  56                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
  57                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  58                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  59                 CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
  60                 CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
  61                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  62                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  63
  64                 vector<string> myArray;
  65                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  66                 return myArray;
  67         }
  68         catch(exception& e) {
  69                 m->errorOut(e, "MatrixOutputCommand", "setParameters");
  70                 exit(1);
  71         }
  72 }
  73 //**********************************************************************************************************************
  74 string MatrixOutputCommand::getHelpString(){
  75         try {
  76                 string helpString = "";
  77                 ValidCalculators validCalculator;
  78                 helpString += "The dist.shared command parameters are shared, groups, calc, output and label.  shared is a required, unless you have a valid current file.\n";
  79                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
  80                 helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n";
  81                 helpString += "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
  82                 helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n";
  83                 helpString += "Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n";
  84                 helpString += "The default value for groups is all the groups in your groupfile.\n";
  85                 helpString += "The default value for calc is jclass and thetayc.\n";
  86                 helpString += validCalculator.printCalc("matrix");
  87                 helpString += "The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\n";
  88                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  89                 return helpString;
  90         }
  91         catch(exception& e) {
  92                 m->errorOut(e, "MatrixOutputCommand", "getHelpString");
  93                 exit(1);
  94         }
  95 }
  96 //**********************************************************************************************************************
  97 MatrixOutputCommand::MatrixOutputCommand(){
  98         try {
  99                 abort = true; calledHelp = true;
 100                 setParameters();
 101                 vector<string> tempOutNames;
 102                 outputTypes["phylip"] = tempOutNames;
 103         }
 104         catch(exception& e) {
 105                 m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
 106                 exit(1);
 107         }
 108 }
 109 //**********************************************************************************************************************
 110
 111 MatrixOutputCommand::MatrixOutputCommand(string option)  {
 112         try {
 113                 abort = false; calledHelp = false;
 114                 allLines = 1;
 115
 116                 //allow user to run help
 117                 if(option == "help") {  help(); abort = true; calledHelp = true; }
 118                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 119
 120                 else {
 121                         vector<string> myArray = setParameters();
 122
 123                         OptionParser parser(option);
 124                         map<string,string> parameters  = parser.getParameters();
 125                         map<string,string>::iterator it;
 126
 127                         ValidParameters validParameter;
 128
 129                         //check to make sure all parameters are valid for command
 130                         for (it = parameters.begin(); it != parameters.end(); it++) {
 131                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 132                         }
 133
 134                         //initialize outputTypes
 135                         vector<string> tempOutNames;
 136                         outputTypes["phylip"] = tempOutNames;
 137
 138                         //if the user changes the input directory command factory will send this info to us in the output parameter
 139                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 140                         if (inputDir == "not found"){   inputDir = "";          }
 141                         else {
 142                                 string path;
 143                                 it = parameters.find("shared");
 144                                 //user has given a template file
 145                                 if(it != parameters.end()){
 146                                         path = m->hasPath(it->second);
 147                                         //if the user has not given a path then, add inputdir. else leave path alone.
 148                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 149                                 }
 150                         }
 151
 152                         sharedfile = validParameter.validFile(parameters, "shared", true);
 153                         if (sharedfile == "not found") {
 154                                 //if there is a current shared file, use it
 155                                 sharedfile = m->getSharedFile();
 156                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 157                                 else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 158                         }else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 159
 160                         //if the user changes the output directory command factory will send this info to us in the output parameter
 161                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 162                                 outputDir = "";
 163                                 outputDir += m->hasPath(sharedfile); //if user entered a file with a path then preserve it
 164                         }
 165
 166                         //check for optional parameter and set defaults
 167                         // ...at some point should added some additional type checking...
 168                         label = validParameter.validFile(parameters, "label", false);
 169                         if (label == "not found") { label = ""; }
 170                         else {
 171                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 172                                 else { allLines = 1;  }
 173                         }
 174
 175                         output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "lt"; }
 176                         if ((output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
 177
 178                         groups = validParameter.validFile(parameters, "groups", false);
 179                         if (groups == "not found") { groups = ""; }
 180                         else {
 181                                 m->splitAtDash(groups, Groups);
 182                                 m->Groups = Groups;
 183                         }
 184
 185                         calc = validParameter.validFile(parameters, "calc", false);
 186                         if (calc == "not found") { calc = "jclass-thetayc";  }
 187                         else {
 188                                  if (calc == "default")  {  calc = "jclass-thetayc";  }
 189                         }
 190                         m->splitAtDash(calc, Estimators);
 191                         if (m->inUsersGroups("citation", Estimators)) {
 192                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 193                                 //remove citation from list of calcs
 194                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 195                         }
 196
 197                         if (abort == false) {
 198
 199                                 ValidCalculators validCalculator;
 200
 201                                 int i;
 202                                 for (i=0; i<Estimators.size(); i++) {
 203                                         if (validCalculator.isValidCalculator("matrix", Estimators[i]) == true) {
 204                                                 if (Estimators[i] == "sharedsobs") {
 205                                                         matrixCalculators.push_back(new SharedSobsCS());
 206                                                 }else if (Estimators[i] == "sharedchao") {
 207                                                         matrixCalculators.push_back(new SharedChao1());
 208                                                 }else if (Estimators[i] == "sharedace") {
 209                                                         matrixCalculators.push_back(new SharedAce());
 210                                                 }else if (Estimators[i] == "jabund") {
 211                                                         matrixCalculators.push_back(new JAbund());
 212                                                 }else if (Estimators[i] == "sorabund") {
 213                                                         matrixCalculators.push_back(new SorAbund());
 214                                                 }else if (Estimators[i] == "jclass") {
 215                                                         matrixCalculators.push_back(new Jclass());
 216                                                 }else if (Estimators[i] == "sorclass") {
 217                                                         matrixCalculators.push_back(new SorClass());
 218                                                 }else if (Estimators[i] == "jest") {
 219                                                         matrixCalculators.push_back(new Jest());
 220                                                 }else if (Estimators[i] == "sorest") {
 221                                                         matrixCalculators.push_back(new SorEst());
 222                                                 }else if (Estimators[i] == "thetayc") {
 223                                                         matrixCalculators.push_back(new ThetaYC());
 224                                                 }else if (Estimators[i] == "thetan") {
 225                                                         matrixCalculators.push_back(new ThetaN());
 226                                                 }else if (Estimators[i] == "kstest") {
 227                                                         matrixCalculators.push_back(new KSTest());
 228                                                 }else if (Estimators[i] == "sharednseqs") {
 229                                                         matrixCalculators.push_back(new SharedNSeqs());
 230                                                 }else if (Estimators[i] == "ochiai") {
 231                                                         matrixCalculators.push_back(new Ochiai());
 232                                                 }else if (Estimators[i] == "anderberg") {
 233                                                         matrixCalculators.push_back(new Anderberg());
 234                                                 }else if (Estimators[i] == "kulczynski") {
 235                                                         matrixCalculators.push_back(new Kulczynski());
 236                                                 }else if (Estimators[i] == "kulczynskicody") {
 237                                                         matrixCalculators.push_back(new KulczynskiCody());
 238                                                 }else if (Estimators[i] == "lennon") {
 239                                                         matrixCalculators.push_back(new Lennon());
 240                                                 }else if (Estimators[i] == "morisitahorn") {
 241                                                         matrixCalculators.push_back(new MorHorn());
 242                                                 }else if (Estimators[i] == "braycurtis") {
 243                                                         matrixCalculators.push_back(new BrayCurtis());
 244                                                 }else if (Estimators[i] == "whittaker") {
 245                                                         matrixCalculators.push_back(new Whittaker());
 246                                                 }else if (Estimators[i] == "odum") {
 247                                                         matrixCalculators.push_back(new Odum());
 248                                                 }else if (Estimators[i] == "canberra") {
 249                                                         matrixCalculators.push_back(new Canberra());
 250                                                 }else if (Estimators[i] == "structeuclidean") {
 251                                                         matrixCalculators.push_back(new StructEuclidean());
 252                                                 }else if (Estimators[i] == "structchord") {
 253                                                         matrixCalculators.push_back(new StructChord());
 254                                                 }else if (Estimators[i] == "hellinger") {
 255                                                         matrixCalculators.push_back(new Hellinger());
 256                                                 }else if (Estimators[i] == "manhattan") {
 257                                                         matrixCalculators.push_back(new Manhattan());
 258                                                 }else if (Estimators[i] == "structpearson") {
 259                                                         matrixCalculators.push_back(new StructPearson());
 260                                                 }else if (Estimators[i] == "soergel") {
 261                                                         matrixCalculators.push_back(new Soergel());
 262                                                 }else if (Estimators[i] == "spearman") {
 263                                                         matrixCalculators.push_back(new Spearman());
 264                                                 }else if (Estimators[i] == "structkulczynski") {
 265                                                         matrixCalculators.push_back(new StructKulczynski());
 266                                                 }else if (Estimators[i] == "speciesprofile") {
 267                                                         matrixCalculators.push_back(new SpeciesProfile());
 268                                                 }else if (Estimators[i] == "hamming") {
 269                                                         matrixCalculators.push_back(new Hamming());
 270                                                 }else if (Estimators[i] == "structchi2") {
 271                                                         matrixCalculators.push_back(new StructChi2());
 272                                                 }else if (Estimators[i] == "gower") {
 273                                                         matrixCalculators.push_back(new Gower());
 274                                                 }else if (Estimators[i] == "memchi2") {
 275                                                         matrixCalculators.push_back(new MemChi2());
 276                                                 }else if (Estimators[i] == "memchord") {
 277                                                         matrixCalculators.push_back(new MemChord());
 278                                                 }else if (Estimators[i] == "memeuclidean") {
 279                                                         matrixCalculators.push_back(new MemEuclidean());
 280                                                 }else if (Estimators[i] == "mempearson") {
 281                                                         matrixCalculators.push_back(new MemPearson());
 282                                                 }
 283                                         }
 284                                 }
 285
 286                         }
 287                 }
 288
 289         }
 290         catch(exception& e) {
 291                 m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
 292                 exit(1);
 293         }
 294 }
 295
 296 //**********************************************************************************************************************
 297
 298 MatrixOutputCommand::~MatrixOutputCommand(){}
 299
 300 //**********************************************************************************************************************
 301
 302 int MatrixOutputCommand::execute(){
 303         try {
 304
 305                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 306
 307                 //if the users entered no valid calculators don't execute command
 308                 if (matrixCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine();  return 0; }
 309
 310                 input = new InputData(sharedfile, "sharedfile");
 311                 lookup = input->getSharedRAbundVectors();
 312                 string lastLabel = lookup[0]->getLabel();
 313
 314                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 315                 set<string> processedLabels;
 316                 set<string> userLabels = labels;
 317
 318                 if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } return 0;}
 319
 320                 numGroups = lookup.size();
 321
 322                 if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); return 0;  }
 323
 324                 //as long as you are not at the end of the file or done wih the lines you want
 325                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 326
 327                         if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } m->Groups.clear(); return 0;  }
 328
 329                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 330                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 331                                 process(lookup);
 332
 333                                 processedLabels.insert(lookup[0]->getLabel());
 334                                 userLabels.erase(lookup[0]->getLabel());
 335                         }
 336
 337                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 338                                 string saveLabel = lookup[0]->getLabel();
 339
 340                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 341                                 lookup = input->getSharedRAbundVectors(lastLabel);
 342
 343                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 344                                 process(lookup);
 345
 346                                 processedLabels.insert(lookup[0]->getLabel());
 347                                 userLabels.erase(lookup[0]->getLabel());
 348
 349                                 //restore real lastlabel to save below
 350                                 lookup[0]->setLabel(saveLabel);
 351                         }
 352
 353                         lastLabel = lookup[0]->getLabel();
 354
 355                         //get next line to process
 356                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 357                         lookup = input->getSharedRAbundVectors();
 358                 }
 359
 360                 if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } m->Groups.clear(); return 0;  }
 361
 362                 //output error messages about any remaining user labels
 363                 set<string>::iterator it;
 364                 bool needToRun = false;
 365                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 366                         m->mothurOut("Your file does not include the label " + *it);
 367                         if (processedLabels.count(lastLabel) != 1) {
 368                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 369                                 needToRun = true;
 370                         }else {
 371                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 372                         }
 373                 }
 374
 375                 if (m->control_pressed) { outputTypes.clear(); delete input;  for (int i = 0; i < outputNames.size(); i++) {    remove(outputNames[i].c_str()); } m->Groups.clear(); return 0;  }
 376
 377                 //run last label if you need to
 378                 if (needToRun == true)  {
 379                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {  delete lookup[i]; }  }
 380                         lookup = input->getSharedRAbundVectors(lastLabel);
 381
 382                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 383                         process(lookup);
 384                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 385                 }
 386
 387                 if (m->control_pressed) { outputTypes.clear();  delete input;  for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str()); } m->Groups.clear(); return 0;  }
 388
 389                 //reset groups parameter
 390                 m->Groups.clear();
 391
 392                 //set phylip file as new current phylipfile
 393                 string current = "";
 394                 itTypes = outputTypes.find("phylip");
 395                 if (itTypes != outputTypes.end()) {
 396                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
 397                 }
 398
 399                 m->mothurOutEndLine();
 400                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 401                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 402                 m->mothurOutEndLine();
 403
 404
 405                 return 0;
 406         }
 407         catch(exception& e) {
 408                 m->errorOut(e, "MatrixOutputCommand", "execute");
 409                 exit(1);
 410         }
 411 }
 412 /***********************************************************/
 413 void MatrixOutputCommand::printSims(ostream& out) {
 414         try {
 415
 416                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 417
 418                 //output num seqs
 419                 out << simMatrix.size() << endl;
 420
 421                 if (output == "lt") {
 422                         for (int m = 0; m < simMatrix.size(); m++)      {
 423                                 out << lookup[m]->getGroup() << '\t';
 424                                 for (int n = 0; n < m; n++)     {
 425                                         out << simMatrix[m][n] << '\t';
 426                                 }
 427                                 out << endl;
 428                         }
 429                 }else{
 430                         for (int m = 0; m < simMatrix.size(); m++)      {
 431                                 out << lookup[m]->getGroup() << '\t';
 432                                 for (int n = 0; n < simMatrix[m].size(); n++)   {
 433                                         out << simMatrix[m][n] << '\t';
 434                                 }
 435                                 out << endl;
 436                         }
 437                 }
 438         }
 439         catch(exception& e) {
 440                 m->errorOut(e, "MatrixOutputCommand", "printSims");
 441                 exit(1);
 442         }
 443 }
 444 /***********************************************************/
 445 int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
 446         try {
 447
 448                                 EstOutput data;
 449                                 vector<SharedRAbundVector*> subset;
 450
 451                                 //for each calculator
 452                                 for(int i = 0 ; i < matrixCalculators.size(); i++) {
 453
 454                                         //initialize simMatrix
 455                                         simMatrix.clear();
 456                                         simMatrix.resize(numGroups);
 457                                         for (int p = 0; p < simMatrix.size(); p++)      {
 458                                                 for (int j = 0; j < simMatrix.size(); j++)      {
 459                                                         simMatrix[p].push_back(0.0);
 460                                                 }
 461                                         }
 462
 463                                         for (int k = 0; k < thisLookup.size(); k++) {
 464                                                 for (int l = k; l < thisLookup.size(); l++) {
 465                                                         if (k != l) { //we dont need to similiarity of a groups to itself
 466                                                                 //get estimated similarity between 2 groups
 467
 468                                                                 if (m->control_pressed) { return 0; }
 469
 470                                                                 subset.clear(); //clear out old pair of sharedrabunds
 471                                                                 //add new pair of sharedrabunds
 472                                                                 subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
 473
 474                                                                 //if this calc needs all groups to calculate the pair load all groups
 475                                                                 if (matrixCalculators[i]->getNeedsAll()) {
 476                                                                         //load subset with rest of lookup for those calcs that need everyone to calc for a pair
 477                                                                         for (int w = 0; w < thisLookup.size(); w++) {
 478                                                                                 if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
 479                                                                         }
 480                                                                 }
 481
 482                                                                 data = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
 483                                                                 //save values in similarity matrix
 484                                                                 simMatrix[k][l] = 1.0 - data[0];  //convert similiarity to distance
 485                                                                 simMatrix[l][k] = 1.0 - data[0];  //convert similiarity to distance
 486                                                         }
 487                                                 }
 488                                         }
 489
 490                                         exportFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
 491                                         m->openOutputFile(exportFileName, out);
 492                                         outputNames.push_back(exportFileName); outputTypes["phylip"].push_back(exportFileName);
 493
 494                                         printSims(out);
 495                                         out.close();
 496
 497                                 }
 498
 499                                 return 0;
 500
 501         }
 502         catch(exception& e) {
 503                 m->errorOut(e, "MatrixOutputCommand", "process");
 504                 exit(1);
 505         }
 506 }
 507 /***********************************************************/
 508
 509
 510