indicatorcommand.cpp

   1 /*
   2  *  indicatorcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 11/12/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "indicatorcommand.h"
  11 #include "sharedutilities.h"
  12
  13
  14 //**********************************************************************************************************************
  15 vector<string> IndicatorCommand::setParameters(){
  16         try {
  17                 CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
  18                 CommandParameter pdesign("design", "InputTypes", "", "", "TreeDesign", "TreeDesign", "none",false,false); parameters.push_back(pdesign);
  19                 CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(pshared);
  20                 CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(prelabund);
  21                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  22                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  23                 CommandParameter ptree("tree", "InputTypes", "", "", "TreeDesign", "TreeDesign", "none",false,false); parameters.push_back(ptree);
  24                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  25                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  26
  27                 vector<string> myArray;
  28                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  29                 return myArray;
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "IndicatorCommand", "setParameters");
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37 string IndicatorCommand::getHelpString(){
  38         try {
  39                 string helpString = "";
  40                 helpString += "The indicator command reads a shared or relabund file and a tree or design file, and outputs a .indicator.tre and .indicator.summary file. \n";
  41                 helpString += "The new tree contains labels at each internal node.  The label is the node number so you can relate the tree to the summary file.\n";
  42                 helpString += "The summary file lists the indicator value for each OTU for each node.\n";
  43                 helpString += "The indicator command parameters are tree, groups, shared, relabund, design and label. The tree parameter is required as well as either shared or relabund.\n";
  44                 helpString += "The design parameter allows you to provide a design file to relate the tree to the shared or relabund file.\n";
  45                 helpString += "The groups parameter allows you to specify which of the groups in your shared or relabund you would like analyzed, or if you provide a design file the groups in your design file.  The groups may be entered separated by dashes.\n";
  46                 helpString += "The label parameter indicates at what distance your tree relates to the shared or relabund.\n";
  47                 helpString += "The iters parameter allows you to set number of randomization for the P value.  The default is 1000.";
  48                 helpString += "The indicator command should be used in the following format: indicator(tree=test.tre, shared=test.shared, label=0.03)\n";
  49                 helpString += "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n";
  50                 return helpString;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "IndicatorCommand", "getHelpString");
  54                 exit(1);
  55         }
  56 }
  57
  58 //**********************************************************************************************************************
  59 IndicatorCommand::IndicatorCommand(){
  60         try {
  61                 abort = true; calledHelp = true;
  62                 setParameters();
  63                 vector<string> tempOutNames;
  64                 outputTypes["tree"] = tempOutNames;
  65                 outputTypes["summary"] = tempOutNames;
  66         }
  67         catch(exception& e) {
  68                 m->errorOut(e, "IndicatorCommand", "IndicatorCommand");
  69                 exit(1);
  70         }
  71 }
  72 //**********************************************************************************************************************
  73 IndicatorCommand::IndicatorCommand(string option)  {
  74         try {
  75                 abort = false; calledHelp = false;
  76
  77                 //allow user to run help
  78                 if(option == "help") { help(); abort = true; calledHelp = true; }
  79                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  80
  81                 else {
  82                         vector<string> myArray = setParameters();
  83
  84                         OptionParser parser(option);
  85                         map<string, string> parameters = parser.getParameters();
  86
  87                         ValidParameters validParameter;
  88                         map<string, string>::iterator it;
  89
  90                         //check to make sure all parameters are valid for command
  91                         for (it = parameters.begin(); it != parameters.end(); it++) {
  92                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  93                         }
  94
  95                         m->runParse = true;
  96                         m->Groups.clear();
  97                         m->namesOfGroups.clear();
  98                         m->Treenames.clear();
  99                         m->names.clear();
 100
 101                         vector<string> tempOutNames;
 102                         outputTypes["tree"] = tempOutNames;
 103                         outputTypes["summary"] = tempOutNames;
 104
 105                         //if the user changes the input directory command factory will send this info to us in the output parameter
 106                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 107                         if (inputDir == "not found"){   inputDir = "";          }
 108                         else {
 109                                 string path;
 110                                 it = parameters.find("tree");
 111                                 //user has given a template file
 112                                 if(it != parameters.end()){
 113                                         path = m->hasPath(it->second);
 114                                         //if the user has not given a path then, add inputdir. else leave path alone.
 115                                         if (path == "") {       parameters["tree"] = inputDir + it->second;             }
 116                                 }
 117
 118                                 it = parameters.find("shared");
 119                                 //user has given a template file
 120                                 if(it != parameters.end()){
 121                                         path = m->hasPath(it->second);
 122                                         //if the user has not given a path then, add inputdir. else leave path alone.
 123                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 124                                 }
 125
 126                                 it = parameters.find("relabund");
 127                                 //user has given a template file
 128                                 if(it != parameters.end()){
 129                                         path = m->hasPath(it->second);
 130                                         //if the user has not given a path then, add inputdir. else leave path alone.
 131                                         if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
 132                                 }
 133
 134                                 it = parameters.find("design");
 135                                 //user has given a template file
 136                                 if(it != parameters.end()){
 137                                         path = m->hasPath(it->second);
 138                                         //if the user has not given a path then, add inputdir. else leave path alone.
 139                                         if (path == "") {       parameters["design"] = inputDir + it->second;           }
 140                                 }
 141                         }
 142
 143                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 144
 145                         //check for required parameters
 146                         treefile = validParameter.validFile(parameters, "tree", true);
 147                         if (treefile == "not open") { treefile = ""; abort = true; }
 148                         else if (treefile == "not found") { treefile = "";      }
 149                         else { m->setTreeFile(treefile); }
 150
 151                         sharedfile = validParameter.validFile(parameters, "shared", true);
 152                         if (sharedfile == "not open") { abort = true; }
 153                         else if (sharedfile == "not found") { sharedfile = ""; }
 154                         else { inputFileName = sharedfile; m->setSharedFile(sharedfile); }
 155
 156                         relabundfile = validParameter.validFile(parameters, "relabund", true);
 157                         if (relabundfile == "not open") { abort = true; }
 158                         else if (relabundfile == "not found") { relabundfile = ""; }
 159                         else { inputFileName = relabundfile; m->setRelAbundFile(relabundfile); }
 160
 161                         designfile = validParameter.validFile(parameters, "design", true);
 162                         if (designfile == "not open") { designfile = ""; abort = true; }
 163                         else if (designfile == "not found") { designfile = ""; }
 164                         else { m->setDesignFile(designfile); }
 165
 166                         groups = validParameter.validFile(parameters, "groups", false);
 167                         if (groups == "not found") { groups = "";  Groups.push_back("all"); }
 168                         else { m->splitAtDash(groups, Groups);  }
 169                         m->Groups = Groups;
 170
 171                         label = validParameter.validFile(parameters, "label", false);
 172                         if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }
 173
 174                         string temp = validParameter.validFile(parameters, "iters", false);             if (temp == "not found") { temp = "1000"; }
 175                         convert(temp, iters);
 176
 177                         if ((relabundfile == "") && (sharedfile == "")) {
 178                                 //is there are current file available for either of these?
 179                                 //give priority to shared, then relabund
 180                                 sharedfile = m->getSharedFile();
 181                                 if (sharedfile != "") {  inputFileName = sharedfile; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 182                                 else {
 183                                         relabundfile = m->getRelAbundFile();
 184                                         if (relabundfile != "") {  inputFileName = relabundfile; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
 185                                         else {
 186                                                 m->mothurOut("No valid current files. You must provide a shared or relabund."); m->mothurOutEndLine();
 187                                                 abort = true;
 188                                         }
 189                                 }
 190                         }
 191
 192
 193                         if ((designfile == "") && (treefile == "")) {
 194                                 treefile = m->getTreeFile();
 195                                 if (treefile != "") {  m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
 196                                 else {
 197                                         designfile = m->getDesignFile();
 198                                         if (designfile != "") {  m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
 199                                         else {
 200                                                 m->mothurOut("[ERROR]: You must provide either a tree or design file."); m->mothurOutEndLine(); abort = true;
 201                                         }
 202                                 }
 203                         }
 204
 205                         if ((relabundfile != "") && (sharedfile != "")) { m->mothurOut("[ERROR]: You may not use both a shared and relabund file."); m->mothurOutEndLine(); abort = true;  }
 206
 207                 }
 208         }
 209         catch(exception& e) {
 210                 m->errorOut(e, "IndicatorCommand", "IndicatorCommand");
 211                 exit(1);
 212         }
 213 }
 214 //**********************************************************************************************************************
 215
 216 int IndicatorCommand::execute(){
 217         try {
 218
 219                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 220
 221                 cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
 222
 223                 //read designfile if given and set up globaldatas groups for read of sharedfiles
 224                 if (designfile != "") {
 225                         designMap = new GroupMap(designfile);
 226                         designMap->readDesignMap();
 227
 228                         //fill Groups - checks for "all" and for any typo groups
 229                         SharedUtil* util = new SharedUtil();
 230                         util->setGroups(Groups, designMap->namesOfGroups);
 231                         delete util;
 232
 233                         //loop through the Groups and fill Globaldata's Groups with the design file info
 234                         m->Groups = designMap->getNamesSeqs(Groups);
 235                 }
 236
 237                 /***************************************************/
 238                 // use smart distancing to get right sharedRabund  //
 239                 /***************************************************/
 240                 if (sharedfile != "") {
 241                         getShared();
 242                         if (m->control_pressed) { if (designfile != "") { delete designMap; } for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } return 0; }
 243                         if (lookup[0] == NULL) { m->mothurOut("[ERROR] reading shared file."); m->mothurOutEndLine(); return 0; }
 244                 }else {
 245                         getSharedFloat();
 246                         if (m->control_pressed) {  if (designfile != "") { delete designMap; } for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } return 0; }
 247                         if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading relabund file."); m->mothurOutEndLine(); return 0; }
 248                 }
 249
 250                 //reset Globaldatas groups if needed
 251                 if (designfile != "") { m->Groups = Groups; }
 252
 253                 /***************************************************/
 254                 //    reading tree info                                                    //
 255                 /***************************************************/
 256                 if (treefile != "") {
 257                         string groupfile = "";
 258                         m->setTreeFile(treefile);
 259                         Tree* tree = new Tree(treefile); delete tree;  //extracts names from tree to make faked out groupmap
 260                         treeMap = new TreeMap();
 261                         bool mismatch = false;
 262
 263                         for (int i = 0; i < m->Treenames.size(); i++) {
 264                                 //sanity check - is this a group that is not in the sharedfile?
 265                                 if (designfile == "") {
 266                                         if (!(m->inUsersGroups(m->Treenames[i], m->namesOfGroups))) {
 267                                                 m->mothurOut("[ERROR]: " + m->Treenames[i] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
 268                                                 mismatch = true;
 269                                         }
 270                                         treeMap->addSeq(m->Treenames[i], "Group1");
 271                                 }else{
 272                                         vector<string> myGroups; myGroups.push_back(m->Treenames[i]);
 273                                         vector<string> myNames = designMap->getNamesSeqs(myGroups);
 274
 275                                         for(int k = 0; k < myNames.size(); k++) {
 276                                                 if (!(m->inUsersGroups(myNames[k], m->namesOfGroups))) {
 277                                                         m->mothurOut("[ERROR]: " + myNames[k] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
 278                                                         mismatch = true;
 279                                                 }
 280                                         }
 281                                         treeMap->addSeq(m->Treenames[i], "Group1");
 282                                 }
 283                         }
 284
 285                         if ((designfile != "") && (m->Treenames.size() != Groups.size())) { cout << Groups.size() << '\t' << m->Treenames.size() << endl; m->mothurOut("[ERROR]: You design file does not match your tree, aborting."); m->mothurOutEndLine(); mismatch = true; }
 286
 287                         if (mismatch) { //cleanup and exit
 288                                 if (designfile != "") { delete designMap; }
 289                                 if (sharedfile != "") {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } }
 290                                 else { for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } }
 291                                 delete treeMap;
 292                                 return 0;
 293                         }
 294
 295                         read = new ReadNewickTree(treefile);
 296                         int readOk = read->read(treeMap);
 297
 298                         if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete treeMap; delete read; return 0; }
 299
 300                         vector<Tree*> T = read->getTrees();
 301
 302                         delete read;
 303
 304                         if (m->control_pressed) {
 305                                 if (designfile != "") { delete designMap; }
 306                                 if (sharedfile != "") {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } }
 307                                 else { for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } }
 308                                 for (int i = 0; i < T.size(); i++) {  delete T[i];  }  delete treeMap; return 0;
 309                         }
 310
 311                         T[0]->assembleTree();
 312
 313                         /***************************************************/
 314                         //    create ouptut tree - respecting pickedGroups //
 315                         /***************************************************/
 316                         Tree* outputTree = new Tree(m->Groups.size(), treeMap);
 317
 318                         outputTree->getSubTree(T[0], m->Groups);
 319                         outputTree->assembleTree();
 320
 321                         //no longer need original tree, we have output tree to use and label
 322                         for (int i = 0; i < T.size(); i++) {  delete T[i];  }
 323
 324
 325                         if (m->control_pressed) {
 326                                 if (designfile != "") { delete designMap; }
 327                                 if (sharedfile != "") {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } }
 328                                 else { for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } }
 329                                 delete outputTree; delete treeMap;  return 0;
 330                         }
 331
 332                         /***************************************************/
 333                         //              get indicator species values                       //
 334                         /***************************************************/
 335                         GetIndicatorSpecies(outputTree);
 336                         delete outputTree; delete treeMap;
 337
 338                 }else { //run with design file only
 339                         //get indicator species
 340                         GetIndicatorSpecies();
 341                 }
 342
 343                 if (designfile != "") { delete designMap; }
 344                 if (sharedfile != "") {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } }
 345                 else { for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } }
 346
 347                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
 348
 349                 //set tree file as new current treefile
 350                 if (treefile != "") {
 351                         string current = "";
 352                         itTypes = outputTypes.find("tree");
 353                         if (itTypes != outputTypes.end()) {
 354                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
 355                         }
 356                 }
 357                 m->mothurOutEndLine();
 358                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 359                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 360                 m->mothurOutEndLine();
 361
 362                 return 0;
 363         }
 364         catch(exception& e) {
 365                 m->errorOut(e, "IndicatorCommand", "execute");
 366                 exit(1);
 367         }
 368 }
 369 //**********************************************************************************************************************
 370 //divide shared or relabund file by groupings in the design file
 371 //report all otu values to file
 372 int IndicatorCommand::GetIndicatorSpecies(){
 373         try {
 374                 string thisOutputDir = outputDir;
 375                 if (outputDir == "") {  thisOutputDir += m->hasPath(inputFileName);  }
 376                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
 377                 outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
 378
 379                 ofstream out;
 380                 m->openOutputFile(outputFileName, out);
 381                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 382
 383                 int numBins = 0;
 384                 if (sharedfile != "") { numBins = lookup[0]->getNumBins(); }
 385                 else { numBins = lookupFloat[0]->getNumBins(); }
 386
 387                 if (m->control_pressed) { out.close(); return 0; }
 388
 389                 /*****************************************************/
 390                 //create vectors containing rabund info                          //
 391                 /*****************************************************/
 392
 393                 vector<float> indicatorValues; //size of numBins
 394                 vector<float> pValues;
 395                 map< vector<int>, vector<int> > randomGroupingsMap; //maps location in groupings to location in groupings, ie, [0][0] -> [1][2]. This is so we don't have to actually move the sharedRabundVectors.
 396
 397                 if (sharedfile != "") {
 398                         vector< vector<SharedRAbundVector*> > groupings;
 399                         set<string> groupsAlreadyAdded;
 400                         vector<SharedRAbundVector*> subset;
 401
 402                         //for each grouping
 403                         for (int i = 0; i < designMap->namesOfGroups.size(); i++) {
 404
 405                                 for (int k = 0; k < lookup.size(); k++) {
 406                                         //are you from this grouping?
 407                                         if (designMap->getGroup(lookup[k]->getGroup()) == designMap->namesOfGroups[i]) {
 408                                                 subset.push_back(lookup[k]);
 409                                                 groupsAlreadyAdded.insert(lookup[k]->getGroup());
 410                                         }
 411                                 }
 412                                 if (subset.size() != 0) { groupings.push_back(subset); }
 413                                 subset.clear();
 414                         }
 415
 416                         if (groupsAlreadyAdded.size() != lookup.size()) {  m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
 417
 418                         indicatorValues = getValues(groupings, randomGroupingsMap);
 419
 420                         pValues.resize(indicatorValues.size(), 0);
 421                         for(int i=0;i<iters;i++){
 422                                 if (m->control_pressed) { break; }
 423                                 randomGroupingsMap = randomizeGroupings(groupings, lookup.size());
 424                                 vector<float> randomIndicatorValues = getValues(groupings, randomGroupingsMap);
 425
 426                                 for (int j = 0; j < indicatorValues.size(); j++) {
 427                                         if (randomIndicatorValues[j] >= indicatorValues[j]) { pValues[j]++; }
 428                                 }
 429                         }
 430
 431                         for (int i = 0; i < pValues.size(); i++) { pValues[i] /= (double)iters; }
 432
 433                 }else {
 434                         vector< vector<SharedRAbundFloatVector*> > groupings;
 435                         set<string> groupsAlreadyAdded;
 436                         vector<SharedRAbundFloatVector*> subset;
 437
 438                         //for each grouping
 439                         for (int i = 0; i < designMap->namesOfGroups.size(); i++) {
 440                                 for (int k = 0; k < lookupFloat.size(); k++) {
 441                                         //are you from this grouping?
 442                                         if (designMap->getGroup(lookupFloat[k]->getGroup()) == designMap->namesOfGroups[i]) {
 443                                                 subset.push_back(lookupFloat[k]);
 444                                                 groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
 445                                         }
 446                                 }
 447                                 if (subset.size() != 0) { groupings.push_back(subset); }
 448                                 subset.clear();
 449                         }
 450
 451                         if (groupsAlreadyAdded.size() != lookupFloat.size()) {  m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
 452
 453                         indicatorValues = getValues(groupings, randomGroupingsMap);
 454
 455                         pValues.resize(indicatorValues.size(), 0);
 456                         for(int i=0;i<iters;i++){
 457                                 if (m->control_pressed) { break; }
 458                                 randomGroupingsMap = randomizeGroupings(groupings, lookupFloat.size());
 459                                 vector<float> randomIndicatorValues = getValues(groupings, randomGroupingsMap);
 460
 461                                 for (int j = 0; j < indicatorValues.size(); j++) {
 462                                         if (randomIndicatorValues[j] >= indicatorValues[j]) { pValues[j]++; }
 463                                 }
 464                         }
 465
 466                         for (int i = 0; i < pValues.size(); i++) { pValues[i] /= (double)iters; }
 467                 }
 468
 469                 if (m->control_pressed) { out.close(); return 0; }
 470
 471
 472                 /******************************************************/
 473                 //output indicator values to table form               //
 474                 /*****************************************************/
 475                 int indicatorOTU;
 476                 double maxValue, pvalue; maxValue=0.0; pvalue=0.0;
 477                 out << "OTU\tIndicator_Value\tpValue" << endl;
 478                 for (int j = 0; j < indicatorValues.size(); j++) {
 479
 480                         if (m->control_pressed) { out.close(); return 0; }
 481
 482                         out << (j+1) << '\t' << indicatorValues[j] << '\t';
 483
 484                         if (pValues[j] > (1/(float)iters)) { out << pValues[j] << endl; }
 485                         else { out << "<" << (1/(float)iters) << endl; }
 486
 487                         if (maxValue < indicatorValues[j]) {
 488                                 maxValue = indicatorValues[j];
 489                                 indicatorOTU = j;
 490                         }
 491                 }
 492
 493                 m->mothurOutEndLine(); m->mothurOut("Species\tIndicatorValue\tpValue\n");
 494                 cout << "OTU" << indicatorOTU+1 << '\t' << maxValue << '\t';
 495                 string pValueString = "<" + toString((1/(float)iters));
 496                 if (pValues[indicatorOTU] > (1/(float)iters)) { pValueString = toString(pValues[indicatorOTU]); cout << pValues[indicatorOTU];}
 497                 else { cout << "<" << (1/(float)iters); }
 498                 m->mothurOutJustToLog("OTU" + toString(indicatorOTU+1) + "\t" + toString(maxValue) + "\t" + pValueString);
 499                 m->mothurOutEndLine();
 500
 501                 out.close();
 502
 503                 return 0;
 504         }
 505         catch(exception& e) {
 506                 m->errorOut(e, "IndicatorCommand", "GetIndicatorSpecies");
 507                 exit(1);
 508         }
 509 }
 510 //**********************************************************************************************************************
 511 //traverse tree finding indicator species values for each otu at each node
 512 //label node with otu number that has highest indicator value
 513 //report all otu values to file
 514 int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
 515         try {
 516
 517                 string thisOutputDir = outputDir;
 518                 if (outputDir == "") {  thisOutputDir += m->hasPath(inputFileName);  }
 519                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
 520                 outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
 521
 522                 ofstream out;
 523                 m->openOutputFile(outputFileName, out);
 524                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 525
 526                 int numBins = 0;
 527                 if (sharedfile != "") { numBins = lookup[0]->getNumBins(); }
 528                 else { numBins = lookupFloat[0]->getNumBins(); }
 529
 530                 //print headings
 531                 out << "TreeNode\t";
 532                 for (int i = 0; i < numBins; i++) { out << "OTU" << (i+1) << "_IndValue" << '\t' << "pValue" << '\t'; }
 533                 out << endl;
 534
 535                 m->mothurOutEndLine(); m->mothurOut("Node\tSpecies\tIndicatorValue\tpValue\n");
 536
 537                 string treeOutputDir = outputDir;
 538                 if (outputDir == "") {  treeOutputDir += m->hasPath(treefile);  }
 539                 string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "indicator.tre";
 540
 541
 542                 //create a map from tree node index to names of descendants, save time later to know which sharedRabund you need
 543                 map<int, set<string> > nodeToDescendants;
 544                 map<int, set<int> > descendantNodes;
 545                 for (int i = 0; i < T->getNumNodes(); i++) {
 546                         if (m->control_pressed) { return 0; }
 547
 548                         nodeToDescendants[i] = getDescendantList(T, i, nodeToDescendants, descendantNodes);
 549                 }
 550
 551                 //you need the distances to leaf to decide grouping below
 552                 //this will also set branch lengths if the tree does not include them
 553                 map<int, float> distToRoot = getDistToRoot(T);
 554
 555                 //for each node
 556                 for (int i = T->getNumLeaves(); i < T->getNumNodes(); i++) {
 557
 558                         if (m->control_pressed) { out.close(); return 0; }
 559
 560                         /*****************************************************/
 561                         //create vectors containing rabund info                          //
 562                         /*****************************************************/
 563
 564                         vector<float> indicatorValues; //size of numBins
 565                         vector<float> pValues;
 566                         map< vector<int>, vector<int> > randomGroupingsMap; //maps location in groupings to location in groupings, ie, [0][0] -> [1][2]. This is so we don't have to actually move the sharedRabundVectors.
 567
 568                         if (sharedfile != "") {
 569                                 vector< vector<SharedRAbundVector*> > groupings;
 570
 571                                 //get nodes that will be a valid grouping
 572                                 //you are valid if you are not one of my descendants
 573                                 //AND your distToRoot is >= mine
 574                                 //AND you were not added as part of a larger grouping. Largest nodes are added first.
 575
 576                                 set<string> groupsAlreadyAdded;
 577                                 //create a grouping with my grouping
 578                                 vector<SharedRAbundVector*> subset;
 579                                 int count = 0;
 580                                 int doneCount = nodeToDescendants[i].size();
 581                                 for (int k = 0; k < lookup.size(); k++) {
 582                                         //is this descendant of i
 583                                         if ((nodeToDescendants[i].count(lookup[k]->getGroup()) != 0)) {
 584                                                 subset.push_back(lookup[k]);
 585                                                 groupsAlreadyAdded.insert(lookup[k]->getGroup());
 586                                                 count++;
 587                                         }
 588                                         if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
 589                                 }
 590                                 if (subset.size() != 0) { groupings.push_back(subset); }
 591
 592
 593                                 for (int j = (T->getNumNodes()-1); j >= 0; j--) {
 594
 595
 596                                         if ((descendantNodes[i].count(j) == 0) && (distToRoot[j] >= distToRoot[i])) {
 597                                                 vector<SharedRAbundVector*> subset;
 598                                                 int count = 0;
 599                                                 int doneCount = nodeToDescendants[j].size();
 600                                                 for (int k = 0; k < lookup.size(); k++) {
 601                                                         //is this descendant of j, and we didn't already add this as part of a larger grouping
 602                                                         if ((nodeToDescendants[j].count(lookup[k]->getGroup()) != 0) && (groupsAlreadyAdded.count(lookup[k]->getGroup()) == 0)) {
 603                                                                 subset.push_back(lookup[k]);
 604                                                                 groupsAlreadyAdded.insert(lookup[k]->getGroup());
 605                                                                 count++;
 606                                                         }
 607                                                         if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
 608                                                 }
 609
 610                                                 //if subset.size == 0 then the node was added as part of a larger grouping
 611                                                 if (subset.size() != 0) { groupings.push_back(subset); }
 612                                         }
 613                                 }
 614
 615                                 if (groupsAlreadyAdded.size() != lookup.size()) {  m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
 616
 617                                 indicatorValues = getValues(groupings, randomGroupingsMap);
 618
 619                                 pValues.resize(indicatorValues.size(), 0);
 620                                 for(int i=0;i<iters;i++){
 621                                         if (m->control_pressed) { break; }
 622                                         randomGroupingsMap = randomizeGroupings(groupings, lookup.size());
 623                                         vector<float> randomIndicatorValues = getValues(groupings, randomGroupingsMap);
 624
 625                                         for (int j = 0; j < indicatorValues.size(); j++) {
 626                                                 if (randomIndicatorValues[j] >= indicatorValues[j]) { pValues[j]++; }
 627                                         }
 628                                 }
 629
 630                                 for (int i = 0; i < pValues.size(); i++) { pValues[i] /= (double)iters; }
 631
 632                         }else {
 633                                 vector< vector<SharedRAbundFloatVector*> > groupings;
 634
 635                                 //get nodes that will be a valid grouping
 636                                 //you are valid if you are not one of my descendants
 637                                 //AND your distToRoot is >= mine
 638                                 //AND you were not added as part of a larger grouping. Largest nodes are added first.
 639
 640                                 set<string> groupsAlreadyAdded;
 641                                 //create a grouping with my grouping
 642                                 vector<SharedRAbundFloatVector*> subset;
 643                                 int count = 0;
 644                                 int doneCount = nodeToDescendants[i].size();
 645                                 for (int k = 0; k < lookupFloat.size(); k++) {
 646                                         //is this descendant of i
 647                                         if ((nodeToDescendants[i].count(lookupFloat[k]->getGroup()) != 0)) {
 648                                                 subset.push_back(lookupFloat[k]);
 649                                                 groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
 650                                                 count++;
 651                                         }
 652                                         if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
 653                                 }
 654                                 if (subset.size() != 0) { groupings.push_back(subset); }
 655
 656                                 for (int j = (T->getNumNodes()-1); j >= 0; j--) {
 657                                         if ((descendantNodes[i].count(j) == 0) && (distToRoot[j] >= distToRoot[i])) {
 658                                                 vector<SharedRAbundFloatVector*> subset;
 659                                                 int count = 0;
 660                                                 int doneCount = nodeToDescendants[j].size();
 661                                                 for (int k = 0; k < lookupFloat.size(); k++) {
 662                                                         //is this descendant of j, and we didn't already add this as part of a larger grouping
 663                                                         if ((nodeToDescendants[j].count(lookupFloat[k]->getGroup()) != 0) && (groupsAlreadyAdded.count(lookupFloat[k]->getGroup()) == 0)) {
 664                                                                 subset.push_back(lookupFloat[k]);
 665                                                                 groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
 666                                                                 count++;
 667                                                         }
 668                                                         if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
 669                                                 }
 670
 671                                                 //if subset.size == 0 then the node was added as part of a larger grouping
 672                                                 if (subset.size() != 0) { groupings.push_back(subset); }
 673                                         }
 674                                 }
 675
 676                                 if (groupsAlreadyAdded.size() != lookupFloat.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
 677
 678                                 indicatorValues = getValues(groupings, randomGroupingsMap);
 679
 680                                 pValues.resize(indicatorValues.size(), 0);
 681                                 for(int i=0;i<iters;i++){
 682
 683                                         if (m->control_pressed) { break; }
 684                                         randomGroupingsMap = randomizeGroupings(groupings, lookup.size());
 685                                         vector<float> randomIndicatorValues = getValues(groupings, randomGroupingsMap);
 686
 687                                         for (int j = 0; j < indicatorValues.size(); j++) {
 688                                                 if (randomIndicatorValues[j] >= indicatorValues[j]) { pValues[j]++; }
 689                                         }
 690                                 }
 691
 692                                 for (int i = 0; i < pValues.size(); i++) { pValues[i] /= (double)iters; }
 693                         }
 694
 695                         if (m->control_pressed) { out.close(); return 0; }
 696
 697
 698                         /******************************************************/
 699                         //output indicator values to table form + label tree  //
 700                         /*****************************************************/
 701                         out << (i+1) << '\t';
 702                         int indicatorOTU;
 703                         double maxValue, pvalue; maxValue=0.0; pvalue=0.0;
 704                         for (int j = 0; j < indicatorValues.size(); j++) {
 705
 706                                 if (m->control_pressed) { out.close(); return 0; }
 707
 708                                 if (pValues[j] < (1/(float)iters)) {
 709                                         out << indicatorValues[j] << '\t' << '<' << (1/(float)iters) << '\t';
 710                                 }else {
 711                                         out << indicatorValues[j] << '\t' << pValues[j] << '\t';
 712                                 }
 713
 714                                 if (maxValue < indicatorValues[j]) {
 715                                         maxValue = indicatorValues[j];
 716                                         indicatorOTU = j;
 717                                 }
 718                         }
 719                         out << endl;
 720
 721                         T->tree[i].setLabel((i+1));
 722
 723                         cout << i+1 << "\tOTU" << indicatorOTU+1 << '\t' << maxValue << '\t';
 724                         string pValueString = "<" + toString((1/(float)iters));
 725                         if (pValues[indicatorOTU] > (1/(float)iters)) { pValueString = toString(pValues[indicatorOTU]); cout << pValues[indicatorOTU];}
 726                         else { cout << "<" << (1/(float)iters); }
 727                         m->mothurOutJustToLog(toString(i) + "\tOTU" + toString(indicatorOTU+1) + "\t" + toString(maxValue) + "\t" + pValueString);
 728                         m->mothurOutEndLine();
 729
 730
 731                 }
 732                 out.close();
 733
 734                 ofstream outTree;
 735                 m->openOutputFile(outputTreeFileName, outTree);
 736                 outputNames.push_back(outputTreeFileName); outputTypes["tree"].push_back(outputTreeFileName);
 737
 738                 T->print(outTree, "both");
 739                 outTree.close();
 740
 741                 return 0;
 742         }
 743         catch(exception& e) {
 744                 m->errorOut(e, "IndicatorCommand", "GetIndicatorSpecies");
 745                 exit(1);
 746         }
 747 }
 748 //**********************************************************************************************************************
 749 vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundFloatVector*> >& groupings, map< vector<int>, vector<int> > groupingsMap){
 750         try {
 751                 vector<float> values;
 752                 map< vector<int>, vector<int> >::iterator it;
 753
 754                 //for each otu
 755                 for (int i = 0; i < groupings[0][0]->getNumBins(); i++) {
 756
 757                         if (m->control_pressed) { return values; }
 758
 759                         vector<float> terms;
 760                         float AijDenominator = 0.0;
 761                         vector<float> Bij;
 762
 763                         //get overall abundance of each grouping
 764                         for (int j = 0; j < groupings.size(); j++) {
 765
 766                                 float totalAbund = 0;
 767                                 int numNotZero = 0;
 768                                 for (int k = 0; k < groupings[j].size(); k++) {
 769                                         vector<int> temp; temp.push_back(j); temp.push_back(k);
 770                                         it = groupingsMap.find(temp);
 771
 772                                         if (it == groupingsMap.end()) { //this one didnt get moved
 773                                                 totalAbund += groupings[j][k]->getAbundance(i);
 774                                                 if (groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
 775                                         }else {
 776                                                 totalAbund += groupings[(it->second)[0]][(it->second)[1]]->getAbundance(i);
 777                                                 if (groupings[(it->second)[0]][(it->second)[1]]->getAbundance(i) != 0.0) { numNotZero++; }
 778                                         }
 779
 780                                 }
 781
 782                                 //mean abundance
 783                                 float Aij = (totalAbund / (float) groupings[j].size());
 784                                 terms.push_back(Aij);
 785
 786                                 //percentage of sites represented
 787                                 Bij.push_back(numNotZero / (float) groupings[j].size());
 788
 789                                 AijDenominator += Aij;
 790                         }
 791
 792                         float maxIndVal = 0.0;
 793                         for (int j = 0; j < terms.size(); j++) {
 794                                 float thisAij = (terms[j] / AijDenominator); //relative abundance
 795                                 float thisValue = thisAij * Bij[j] * 100.0;
 796
 797                                 //save largest
 798                                 if (thisValue > maxIndVal) { maxIndVal = thisValue; }
 799                         }
 800
 801                         values.push_back(maxIndVal);
 802                 }
 803
 804                 return values;
 805         }
 806         catch(exception& e) {
 807                 m->errorOut(e, "IndicatorCommand", "getValues");
 808                 exit(1);
 809         }
 810 }
 811 //**********************************************************************************************************************
 812 //same as above, just data type difference
 813 vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundVector*> >& groupings, map< vector<int>, vector<int> > groupingsMap){
 814         try {
 815                 vector<float> values;
 816
 817         /*for (int j = 0; j < groupings.size(); j++) {
 818                 cout << "grouping " << j << endl;
 819                 for (int k = 0; k < groupings[j].size(); k++) {
 820                         cout << groupings[j][k]->getGroup() << endl;
 821                 }
 822         }*/
 823                 map< vector<int>, vector<int> >::iterator it;
 824
 825                 //for each otu
 826                 for (int i = 0; i < groupings[0][0]->getNumBins(); i++) {
 827                         vector<float> terms;
 828                         float AijDenominator = 0.0;
 829                         vector<float> Bij;
 830                         //get overall abundance of each grouping
 831                         for (int j = 0; j < groupings.size(); j++) {
 832
 833                                 int totalAbund = 0.0;
 834                                 int numNotZero = 0;
 835                                 for (int k = 0; k < groupings[j].size(); k++) {
 836                                         vector<int> temp; temp.push_back(j); temp.push_back(k);
 837                                         it = groupingsMap.find(temp);
 838
 839                                         if (it == groupingsMap.end()) { //this one didnt get moved
 840                                                 totalAbund += groupings[j][k]->getAbundance(i);
 841                                                 if (groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
 842                                         }else {
 843                                                 totalAbund += groupings[(it->second)[0]][(it->second)[1]]->getAbundance(i);
 844                                                 if (groupings[(it->second)[0]][(it->second)[1]]->getAbundance(i) != 0.0) { numNotZero++; }
 845                                         }
 846
 847                                 }
 848
 849                                 //mean abundance
 850                                 float Aij = (totalAbund / (float) groupings[j].size());
 851                                 terms.push_back(Aij);
 852
 853                                 //percentage of sites represented
 854                                 Bij.push_back(numNotZero / (float) groupings[j].size());
 855
 856                                 AijDenominator += Aij;
 857                         }
 858
 859                         float maxIndVal = 0.0;
 860                         for (int j = 0; j < terms.size(); j++) {
 861                                 float thisAij = (terms[j] / AijDenominator); //relative abundance
 862                                 float thisValue = thisAij * Bij[j] * 100.0;
 863
 864                                 //save largest
 865                                 if (thisValue > maxIndVal) { maxIndVal = thisValue; }
 866                         }
 867
 868                         values.push_back(maxIndVal);
 869                 }
 870
 871                 return values;
 872         }
 873         catch(exception& e) {
 874                 m->errorOut(e, "IndicatorCommand", "getValues");
 875                 exit(1);
 876         }
 877 }
 878 //**********************************************************************************************************************
 879 //you need the distances to root to decide groupings
 880 //this will also set branch lengths if the tree does not include them
 881 map<int, float> IndicatorCommand::getDistToRoot(Tree*& T){
 882         try {
 883                 map<int, float> dists;
 884
 885                 bool hasBranchLengths = false;
 886                 for (int i = 0; i < T->getNumNodes(); i++) {
 887                         if (T->tree[i].getBranchLength() > 0.0) {  hasBranchLengths = true; break; }
 888                 }
 889
 890                 //set branchlengths if needed
 891                 if (!hasBranchLengths) {
 892                         for (int i = 0; i < T->getNumNodes(); i++) {
 893
 894                                 int lc = T->tree[i].getLChild();
 895                                 int rc = T->tree[i].getRChild();
 896
 897                                 if (lc == -1) { // you are a leaf
 898                                         //if you are a leaf set you priliminary length to 1.0, this may adjust later
 899                                         T->tree[i].setBranchLength(1.0);
 900                                         dists[i] = 1.0;
 901                                 }else{ // you are an internal node
 902                                         //look at your children's length to leaf
 903                                         float ldist = dists[lc];
 904                                         float rdist = dists[rc];
 905
 906                                         float greater = ldist;
 907                                         if (rdist > greater) { greater = rdist; dists[i] = ldist + 1.0;}
 908                                         else { dists[i] = rdist + 1.0; }
 909
 910
 911                                         //branch length = difference + 1
 912                                         T->tree[lc].setBranchLength((abs(ldist-greater) + 1.0));
 913                                         T->tree[rc].setBranchLength((abs(rdist-greater) + 1.0));
 914                                 }
 915                         }
 916                 }
 917
 918                 dists.clear();
 919
 920                 for (int i = 0; i < T->getNumNodes(); i++) {
 921
 922                         double sum = 0.0;
 923                         int index = i;
 924
 925                         while(T->tree[index].getParent() != -1){
 926                                 if (T->tree[index].getBranchLength() != -1) {
 927                                         sum += abs(T->tree[index].getBranchLength());
 928                                 }
 929                                 index = T->tree[index].getParent();
 930                         }
 931
 932                         dists[i] = sum;
 933                 }
 934
 935                 return dists;
 936         }
 937         catch(exception& e) {
 938                 m->errorOut(e, "IndicatorCommand", "getLengthToLeaf");
 939                 exit(1);
 940         }
 941 }
 942 //**********************************************************************************************************************
 943 set<string> IndicatorCommand::getDescendantList(Tree*& T, int i, map<int, set<string> > descendants, map<int, set<int> >& nodes){
 944         try {
 945                 set<string> names;
 946
 947                 set<string>::iterator it;
 948
 949                 int lc = T->tree[i].getLChild();
 950                 int rc = T->tree[i].getRChild();
 951
 952                 if (lc == -1) { //you are a leaf your only descendant is yourself
 953                         set<int> temp; temp.insert(i);
 954                         nodes[i] = temp;
 955
 956                         if (designfile == "") {
 957                                 names.insert(T->tree[i].getName());
 958                         }else {
 959                                 vector<string> myGroup; myGroup.push_back(T->tree[i].getName());
 960                                 vector<string> myReps = designMap->getNamesSeqs(myGroup);
 961                                 for (int k = 0; k < myReps.size(); k++) {
 962                                         names.insert(myReps[k]);
 963                                 }
 964                         }
 965
 966                 }else{ //your descedants are the combination of your childrens descendants
 967                         names = descendants[lc];
 968                         nodes[i] = nodes[lc];
 969                         for (it = descendants[rc].begin(); it != descendants[rc].end(); it++) {
 970                                 names.insert(*it);
 971                         }
 972                         for (set<int>::iterator itNum = nodes[rc].begin(); itNum != nodes[rc].end(); itNum++) {
 973                                 nodes[i].insert(*itNum);
 974                         }
 975                         //you are your own descendant
 976                         nodes[i].insert(i);
 977                 }
 978
 979                 return names;
 980         }
 981         catch(exception& e) {
 982                 m->errorOut(e, "IndicatorCommand", "getDescendantList");
 983                 exit(1);
 984         }
 985 }
 986 //**********************************************************************************************************************
 987 int IndicatorCommand::getShared(){
 988         try {
 989                 InputData* input = new InputData(sharedfile, "sharedfile");
 990                 lookup = input->getSharedRAbundVectors();
 991                 string lastLabel = lookup[0]->getLabel();
 992
 993                 if (label == "") { label = lastLabel; delete input; return 0; }
 994
 995                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 996                 set<string> labels; labels.insert(label);
 997                 set<string> processedLabels;
 998                 set<string> userLabels = labels;
 999
1000                 //as long as you are not at the end of the file or done wih the lines you want
1001                 while((lookup[0] != NULL) && (userLabels.size() != 0)) {
1002                         if (m->control_pressed) {  delete input; return 0;  }
1003
1004                         if(labels.count(lookup[0]->getLabel()) == 1){
1005                                 processedLabels.insert(lookup[0]->getLabel());
1006                                 userLabels.erase(lookup[0]->getLabel());
1007                                 break;
1008                         }
1009
1010                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
1011                                 string saveLabel = lookup[0]->getLabel();
1012
1013                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
1014                                 lookup = input->getSharedRAbundVectors(lastLabel);
1015
1016                                 processedLabels.insert(lookup[0]->getLabel());
1017                                 userLabels.erase(lookup[0]->getLabel());
1018
1019                                 //restore real lastlabel to save below
1020                                 lookup[0]->setLabel(saveLabel);
1021                                 break;
1022                         }
1023
1024                         lastLabel = lookup[0]->getLabel();
1025
1026                         //get next line to process
1027                         //prevent memory leak
1028                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
1029                         lookup = input->getSharedRAbundVectors();
1030                 }
1031
1032
1033                 if (m->control_pressed) { delete input; return 0;  }
1034
1035                 //output error messages about any remaining user labels
1036                 set<string>::iterator it;
1037                 bool needToRun = false;
1038                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
1039                         m->mothurOut("Your file does not include the label " + *it);
1040                         if (processedLabels.count(lastLabel) != 1) {
1041                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
1042                                 needToRun = true;
1043                         }else {
1044                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
1045                         }
1046                 }
1047
1048                 //run last label if you need to
1049                 if (needToRun == true)  {
1050                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i];       } }
1051                         lookup = input->getSharedRAbundVectors(lastLabel);
1052                 }
1053
1054                 delete input;
1055                 return 0;
1056         }
1057         catch(exception& e) {
1058                 m->errorOut(e, "IndicatorCommand", "getShared");
1059                 exit(1);
1060         }
1061 }
1062 //**********************************************************************************************************************
1063 int IndicatorCommand::getSharedFloat(){
1064         try {
1065                 InputData* input = new InputData(relabundfile, "relabund");
1066                 lookupFloat = input->getSharedRAbundFloatVectors();
1067                 string lastLabel = lookupFloat[0]->getLabel();
1068
1069                 if (label == "") { label = lastLabel; delete input; return 0; }
1070
1071                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
1072                 set<string> labels; labels.insert(label);
1073                 set<string> processedLabels;
1074                 set<string> userLabels = labels;
1075
1076                 //as long as you are not at the end of the file or done wih the lines you want
1077                 while((lookupFloat[0] != NULL) && (userLabels.size() != 0)) {
1078
1079                         if (m->control_pressed) {  delete input; return 0;  }
1080
1081                         if(labels.count(lookupFloat[0]->getLabel()) == 1){
1082                                 processedLabels.insert(lookupFloat[0]->getLabel());
1083                                 userLabels.erase(lookupFloat[0]->getLabel());
1084                                 break;
1085                         }
1086
1087                         if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
1088                                 string saveLabel = lookupFloat[0]->getLabel();
1089
1090                                 for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
1091                                 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
1092
1093                                 processedLabels.insert(lookupFloat[0]->getLabel());
1094                                 userLabels.erase(lookupFloat[0]->getLabel());
1095
1096                                 //restore real lastlabel to save below
1097                                 lookupFloat[0]->setLabel(saveLabel);
1098                                 break;
1099                         }
1100
1101                         lastLabel = lookupFloat[0]->getLabel();
1102
1103                         //get next line to process
1104                         //prevent memory leak
1105                         for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
1106                         lookupFloat = input->getSharedRAbundFloatVectors();
1107                 }
1108
1109
1110                 if (m->control_pressed) { delete input; return 0;  }
1111
1112                 //output error messages about any remaining user labels
1113                 set<string>::iterator it;
1114                 bool needToRun = false;
1115                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
1116                         m->mothurOut("Your file does not include the label " + *it);
1117                         if (processedLabels.count(lastLabel) != 1) {
1118                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
1119                                 needToRun = true;
1120                         }else {
1121                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
1122                         }
1123                 }
1124
1125                 //run last label if you need to
1126                 if (needToRun == true)  {
1127                         for (int i = 0; i < lookupFloat.size(); i++) {  if (lookupFloat[i] != NULL) {   delete lookupFloat[i];  } }
1128                         lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
1129                 }
1130
1131                 delete input;
1132                 return 0;
1133         }
1134         catch(exception& e) {
1135                 m->errorOut(e, "IndicatorCommand", "getShared");
1136         exit(1);
1137         }
1138 }
1139 //**********************************************************************************************************************
1140 //swap groups between groupings, in essence randomizing the second column of the design file
1141 map< vector<int>, vector<int> > IndicatorCommand::randomizeGroupings(vector< vector<SharedRAbundVector*> >& groupings, int numLookupGroups){
1142         try {
1143
1144                 map< vector<int>, vector<int> > randomGroupings;
1145
1146                 for (int i = 0; i < numLookupGroups; i++) {
1147                         if (m->control_pressed) {break;}
1148
1149                         //get random groups to swap to switch with
1150                         //generate random int between 0 and groupings.size()-1
1151                         int z = m->getRandomIndex(groupings.size()-1);
1152                         int x = m->getRandomIndex(groupings.size()-1);
1153                         int a = m->getRandomIndex(groupings[z].size()-1);
1154                         int b = m->getRandomIndex(groupings[x].size()-1);
1155                         //cout << i << '\t' << z << '\t' << x << '\t' << a << '\t' << b << endl;
1156                         //if ((z < 0) || (z > 1) || x<0 || x>1 || a <0 || a>groupings[z].size()-1 || b<0 || b>groupings[x].size()-1) { cout << "probelm" << i << '\t' << z << '\t' << x << '\t' << a << '\t' << b << endl;      }
1157
1158                         vector<int> from;
1159                         vector<int> to;
1160
1161                         from.push_back(z); from.push_back(a);
1162                         to.push_back(x); to.push_back(b);
1163
1164                         randomGroupings[from] = to;
1165                 }
1166                 //cout << "done" << endl;
1167                 return randomGroupings;
1168         }
1169         catch(exception& e) {
1170                 m->errorOut(e, "IndicatorCommand", "randomizeGroupings");
1171                 exit(1);
1172         }
1173 }
1174 //**********************************************************************************************************************
1175 //swap groups between groupings, in essence randomizing the second column of the design file
1176 map< vector<int>, vector<int> > IndicatorCommand::randomizeGroupings(vector< vector<SharedRAbundFloatVector*> >& groupings, int numLookupGroups){
1177         try {
1178
1179                 map< vector<int>, vector<int> > randomGroupings;
1180
1181                 for (int i = 0; i < numLookupGroups; i++) {
1182
1183                         //get random groups to swap to switch with
1184                         //generate random int between 0 and groupings.size()-1
1185                         int z = m->getRandomIndex(groupings.size()-1);
1186                         int x = m->getRandomIndex(groupings.size()-1);
1187                         int a = m->getRandomIndex(groupings[z].size()-1);
1188                         int b = m->getRandomIndex(groupings[x].size()-1);
1189                         //cout << i << '\t' << z << '\t' << x << '\t' << a << '\t' << b << endl;
1190
1191                         vector<int> from;
1192                         vector<int> to;
1193
1194                         from.push_back(z); from.push_back(a);
1195                         to.push_back(x); to.push_back(b);
1196
1197                         randomGroupings[from] = to;
1198                 }
1199
1200                 return randomGroupings;
1201         }
1202         catch(exception& e) {
1203                 m->errorOut(e, "IndicatorCommand", "randomizeGroupings");
1204                 exit(1);
1205         }
1206 }
1207
1208 /*****************************************************************/
1209
1210