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 vector<string> IndicatorCommand::getValidParameters(){
  15         try {
  16                 string Array[] =  {"tree","shared","relabund","design","label","groups","outputdir","inputdir"};
  17                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "IndicatorCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 vector<string> IndicatorCommand::getRequiredParameters(){
  27         try {
  28                 string Array[] =  {"tree"};
  29                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  30                 return myArray;
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "IndicatorCommand", "getRequiredParameters");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 IndicatorCommand::IndicatorCommand(){
  39         try {
  40                 abort = true; calledHelp = true;
  41                 vector<string> tempOutNames;
  42                 outputTypes["tree"] = tempOutNames;
  43                 outputTypes["summary"] = tempOutNames;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "IndicatorCommand", "IndicatorCommand");
  47                 exit(1);
  48         }
  49 }
  50
  51 //**********************************************************************************************************************
  52 vector<string> IndicatorCommand::getRequiredFiles(){
  53         try {
  54                 vector<string> myArray;
  55                 return myArray;
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "IndicatorCommand", "getRequiredFiles");
  59                 exit(1);
  60         }
  61 }
  62 //**********************************************************************************************************************
  63 IndicatorCommand::IndicatorCommand(string option)  {
  64         try {
  65                 globaldata = GlobalData::getInstance();
  66                 abort = false; calledHelp = false;
  67
  68                 //allow user to run help
  69                 if(option == "help") { help(); abort = true; calledHelp = true; }
  70
  71                 else {
  72                         //valid paramters for this command
  73                         string Array[] =  {"tree","shared","design","relabund","groups","label","outputdir","inputdir"};
  74                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  75
  76                         OptionParser parser(option);
  77                         map<string, string> parameters = parser.getParameters();
  78
  79                         ValidParameters validParameter;
  80                         map<string, string>::iterator it;
  81
  82                         //check to make sure all parameters are valid for command
  83                         for (it = parameters.begin(); it != parameters.end(); it++) {
  84                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  85                         }
  86
  87                         globaldata->newRead();
  88
  89                         vector<string> tempOutNames;
  90                         outputTypes["tree"] = tempOutNames;
  91                         outputTypes["summary"] = tempOutNames;
  92
  93                         //if the user changes the input directory command factory will send this info to us in the output parameter
  94                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  95                         if (inputDir == "not found"){   inputDir = "";          }
  96                         else {
  97                                 string path;
  98                                 it = parameters.find("tree");
  99                                 //user has given a template file
 100                                 if(it != parameters.end()){
 101                                         path = m->hasPath(it->second);
 102                                         //if the user has not given a path then, add inputdir. else leave path alone.
 103                                         if (path == "") {       parameters["tree"] = inputDir + it->second;             }
 104                                 }
 105
 106                                 it = parameters.find("shared");
 107                                 //user has given a template file
 108                                 if(it != parameters.end()){
 109                                         path = m->hasPath(it->second);
 110                                         //if the user has not given a path then, add inputdir. else leave path alone.
 111                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 112                                 }
 113
 114                                 it = parameters.find("relabund");
 115                                 //user has given a template file
 116                                 if(it != parameters.end()){
 117                                         path = m->hasPath(it->second);
 118                                         //if the user has not given a path then, add inputdir. else leave path alone.
 119                                         if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
 120                                 }
 121
 122                                 it = parameters.find("design");
 123                                 //user has given a template file
 124                                 if(it != parameters.end()){
 125                                         path = m->hasPath(it->second);
 126                                         //if the user has not given a path then, add inputdir. else leave path alone.
 127                                         if (path == "") {       parameters["design"] = inputDir + it->second;           }
 128                                 }
 129                         }
 130
 131                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 132
 133                         //check for required parameters
 134                         treefile = validParameter.validFile(parameters, "tree", true);
 135                         if (treefile == "not open") { abort = true; }
 136                         else if (treefile == "not found") { treefile = ""; m->mothurOut("tree is a required parameter for the indicator command."); m->mothurOutEndLine(); abort = true;  }
 137                         else {  globaldata->setTreeFile(treefile);  globaldata->setFormat("tree");      }
 138
 139                         sharedfile = validParameter.validFile(parameters, "shared", true);
 140                         if (sharedfile == "not open") { abort = true; }
 141                         else if (sharedfile == "not found") { sharedfile = ""; }
 142                         else { inputFileName = sharedfile; }
 143
 144                         relabundfile = validParameter.validFile(parameters, "relabund", true);
 145                         if (relabundfile == "not open") { abort = true; }
 146                         else if (relabundfile == "not found") { relabundfile = ""; }
 147                         else { inputFileName = relabundfile; }
 148
 149                         designfile = validParameter.validFile(parameters, "design", true);
 150                         if (designfile == "not open") { abort = true; }
 151                         else if (designfile == "not found") { designfile = ""; }
 152
 153                         groups = validParameter.validFile(parameters, "groups", false);
 154                         if (groups == "not found") { groups = "";  Groups.push_back("all"); }
 155                         else { m->splitAtDash(groups, Groups);  }
 156                         globaldata->Groups = Groups;
 157
 158                         label = validParameter.validFile(parameters, "label", false);
 159                         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=""; }
 160
 161                         if ((relabundfile == "") && (sharedfile == "")) { m->mothurOut("You must provide either a shared or relabund file."); m->mothurOutEndLine(); abort = true;  }
 162
 163                         if ((relabundfile != "") && (sharedfile != "")) { m->mothurOut("You may not use both a shared and relabund file."); m->mothurOutEndLine(); abort = true;  }
 164
 165                 }
 166         }
 167         catch(exception& e) {
 168                 m->errorOut(e, "IndicatorCommand", "IndicatorCommand");
 169                 exit(1);
 170         }
 171 }
 172 //**********************************************************************************************************************
 173
 174 void IndicatorCommand::help(){
 175         try {
 176                 m->mothurOut("The indicator command reads a shared or relabund file and a tree file, and outputs a .indicator.tre and .indicator.summary file. \n");
 177                 m->mothurOut("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");
 178                 m->mothurOut("The summary file lists the indicator value for each OTU for each node.\n");
 179                 m->mothurOut("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");
 180                 m->mothurOut("The design parameter allows you to provide a design file to relate the tree to the shared or relabund file.\n");
 181                 m->mothurOut("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");
 182                 m->mothurOut("The label parameter indicates at what distance your tree relates to the shared or relabund.\n");
 183                 m->mothurOut("The indicator command should be used in the following format: indicator(tree=test.tre, shared=test.shared, label=0.03)\n");
 184                 m->mothurOut("Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n");
 185         }
 186         catch(exception& e) {
 187                 m->errorOut(e, "IndicatorCommand", "help");
 188                 exit(1);
 189         }
 190 }
 191
 192 //**********************************************************************************************************************
 193
 194 IndicatorCommand::~IndicatorCommand(){}
 195
 196 //**********************************************************************************************************************
 197
 198 int IndicatorCommand::execute(){
 199         try {
 200
 201                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 202
 203                 //read designfile if given and set up globaldatas groups for read of sharedfiles
 204                 if (designfile != "") {
 205                         designMap = new GroupMap(designfile);
 206                         designMap->readDesignMap();
 207
 208                         //fill Groups - checks for "all" and for any typo groups
 209                         SharedUtil* util = new SharedUtil();
 210                         util->setGroups(Groups, designMap->namesOfGroups);
 211                         delete util;
 212
 213                         //loop through the Groups and fill Globaldata's Groups with the design file info
 214                         globaldata->Groups = designMap->getNamesSeqs(Groups);
 215                 }
 216
 217                 /***************************************************/
 218                 // use smart distancing to get right sharedRabund  //
 219                 /***************************************************/
 220                 if (sharedfile != "") {
 221                         getShared();
 222                         if (m->control_pressed) { if (designfile != "") { delete designMap; } for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } return 0; }
 223                         if (lookup[0] == NULL) { m->mothurOut("[ERROR] reading shared file."); m->mothurOutEndLine(); return 0; }
 224                 }else {
 225                         getSharedFloat();
 226                         if (m->control_pressed) {  if (designfile != "") { delete designMap; } for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } return 0; }
 227                         if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading relabund file."); m->mothurOutEndLine(); return 0; }
 228                 }
 229
 230                 //reset Globaldatas groups if needed
 231                 if (designfile != "") { globaldata->Groups = Groups; }
 232
 233                 /***************************************************/
 234                 //    reading tree info                                                    //
 235                 /***************************************************/
 236                 string groupfile = "";
 237                 Tree* tree = new Tree(treefile); delete tree;  //extracts names from tree to make faked out groupmap
 238
 239                 globaldata->setGroupFile(groupfile);
 240                 treeMap = new TreeMap();
 241                 bool mismatch = false;
 242
 243                 for (int i = 0; i < globaldata->Treenames.size(); i++) {
 244                         //sanity check - is this a group that is not in the sharedfile?
 245                         if (designfile == "") {
 246                                 if (!(m->inUsersGroups(globaldata->Treenames[i], globaldata->gGroupmap->namesOfGroups))) {
 247                                         m->mothurOut("[ERROR]: " + globaldata->Treenames[i] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
 248                                         mismatch = true;
 249                                 }
 250                                 treeMap->addSeq(globaldata->Treenames[i], "Group1");
 251                         }else{
 252                                 vector<string> myGroups; myGroups.push_back(globaldata->Treenames[i]);
 253                                 vector<string> myNames = designMap->getNamesSeqs(myGroups);
 254
 255                                 for(int k = 0; k < myNames.size(); k++) {
 256                                         if (!(m->inUsersGroups(myNames[k], globaldata->gGroupmap->namesOfGroups))) {
 257                                                 m->mothurOut("[ERROR]: " + myNames[k] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
 258                                                 mismatch = true;
 259                                         }
 260                                 }
 261                                 treeMap->addSeq(globaldata->Treenames[i], "Group1");
 262                         }
 263                 }
 264
 265                 if ((designfile != "") && (globaldata->Treenames.size() != Groups.size())) { m->mothurOut("[ERROR]: You design file does not match your tree, aborting."); m->mothurOutEndLine(); mismatch = true; }
 266
 267                 if (mismatch) { //cleanup and exit
 268                         if (designfile != "") { delete designMap; }
 269                         if (sharedfile != "") {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } }
 270                         else { for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } }
 271                         delete treeMap;
 272                         return 0;
 273                 }
 274
 275                 globaldata->gTreemap = treeMap;
 276
 277                 read = new ReadNewickTree(treefile);
 278                 int readOk = read->read();
 279
 280                 if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); globaldata->gTree.clear(); delete globaldata->gTreemap; delete read; return 0; }
 281
 282                 vector<Tree*> T = globaldata->gTree;
 283
 284                 delete read;
 285
 286                 if (m->control_pressed) {
 287                         if (designfile != "") { delete designMap; }
 288                         if (sharedfile != "") {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } }
 289                         else { for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } }
 290                         for (int i = 0; i < T.size(); i++) {  delete T[i];  } globaldata->gTree.clear(); delete globaldata->gTreemap; return 0;
 291                 }
 292
 293                 T[0]->assembleTree();
 294
 295                 /***************************************************/
 296                 //    create ouptut tree - respecting pickedGroups //
 297                 /***************************************************/
 298                 Tree* outputTree = new Tree(globaldata->Groups.size());
 299
 300                 outputTree->getSubTree(T[0], globaldata->Groups);
 301                 outputTree->assembleTree();
 302
 303                 //no longer need original tree, we have output tree to use and label
 304                 for (int i = 0; i < T.size(); i++) {  delete T[i];  } globaldata->gTree.clear();
 305
 306
 307                 if (m->control_pressed) {
 308                         if (designfile != "") { delete designMap; }
 309                         if (sharedfile != "") {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } }
 310                         else { for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } }
 311                         delete outputTree; delete globaldata->gTreemap;  return 0;
 312                 }
 313
 314                 /***************************************************/
 315                 //              get indicator species values                       //
 316                 /***************************************************/
 317                 GetIndicatorSpecies(outputTree);
 318
 319                 if (designfile != "") { delete designMap; }
 320
 321                 if (m->control_pressed) {
 322                         if (sharedfile != "") {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } }
 323                         else { for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } }
 324                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 325                         delete outputTree; delete globaldata->gTreemap;  return 0;
 326                 }
 327
 328                 //set tree file as new current treefile
 329                 string current = "";
 330                 itTypes = outputTypes.find("tree");
 331                 if (itTypes != outputTypes.end()) {
 332                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
 333                 }
 334
 335                 m->mothurOutEndLine();
 336                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 337                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 338                 m->mothurOutEndLine();
 339
 340                 return 0;
 341         }
 342         catch(exception& e) {
 343                 m->errorOut(e, "IndicatorCommand", "execute");
 344                 exit(1);
 345         }
 346 }
 347 //**********************************************************************************************************************
 348 //traverse tree finding indicator species values for each otu at each node
 349 //label node with otu number that has highest indicator value
 350 //report all otu values to file
 351 int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
 352         try {
 353
 354                 string thisOutputDir = outputDir;
 355                 if (outputDir == "") {  thisOutputDir += m->hasPath(inputFileName);  }
 356                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
 357                 outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
 358
 359                 ofstream out;
 360                 m->openOutputFile(outputFileName, out);
 361                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 362
 363                 int numBins = 0;
 364                 if (sharedfile != "") { numBins = lookup[0]->getNumBins(); }
 365                 else { numBins = lookupFloat[0]->getNumBins(); }
 366
 367                 //print headings
 368                 out << "TreeNode\t";
 369                 for (int i = 0; i < numBins; i++) { out << "OTU-" << (i+1) << '\t'; }
 370                 out << endl;
 371
 372                 string treeOutputDir = outputDir;
 373                 if (outputDir == "") {  treeOutputDir += m->hasPath(treefile);  }
 374                 string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "indicator.tre";
 375
 376
 377                 //create a map from tree node index to names of descendants, save time later to know which sharedRabund you need
 378                 map<int, set<string> > nodeToDescendants;
 379                 map<int, set<int> > descendantNodes;
 380                 for (int i = 0; i < T->getNumNodes(); i++) {
 381                         if (m->control_pressed) { return 0; }
 382
 383                         nodeToDescendants[i] = getDescendantList(T, i, nodeToDescendants, descendantNodes);
 384                 }
 385
 386                 //you need the distances to leaf to decide grouping below
 387                 //this will also set branch lengths if the tree does not include them
 388                 map<int, float> distToRoot = getDistToRoot(T);
 389
 390                 //for each node
 391                 for (int i = T->getNumLeaves(); i < T->getNumNodes(); i++) {
 392
 393                         if (m->control_pressed) { out.close(); return 0; }
 394
 395                         /*****************************************************/
 396                         //create vectors containing rabund info                          //
 397                         /*****************************************************/
 398
 399                         vector<float> indicatorValues; //size of numBins
 400
 401                         if (sharedfile != "") {
 402                                 vector< vector<SharedRAbundVector*> > groupings;
 403
 404                                 //get nodes that will be a valid grouping
 405                                 //you are valid if you are not one of my descendants
 406                                 //AND your distToRoot is >= mine
 407                                 //AND you were not added as part of a larger grouping. Largest nodes are added first.
 408
 409                                 set<string> groupsAlreadyAdded;
 410                                 //create a grouping with my grouping
 411                                 vector<SharedRAbundVector*> subset;
 412                                 int count = 0;
 413                                 int doneCount = nodeToDescendants[i].size();
 414                                 for (int k = 0; k < lookup.size(); k++) {
 415                                         //is this descendant of i
 416                                         if ((nodeToDescendants[i].count(lookup[k]->getGroup()) != 0)) {
 417                                                 subset.push_back(lookup[k]);
 418                                                 groupsAlreadyAdded.insert(lookup[k]->getGroup());
 419                                                 count++;
 420                                         }
 421                                         if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
 422                                 }
 423                                 if (subset.size() != 0) { groupings.push_back(subset); }
 424
 425
 426                                 for (int j = (T->getNumNodes()-1); j >= 0; j--) {
 427
 428
 429                                         if ((descendantNodes[i].count(j) == 0) && (distToRoot[j] >= distToRoot[i])) {
 430                                                 vector<SharedRAbundVector*> subset;
 431                                                 int count = 0;
 432                                                 int doneCount = nodeToDescendants[j].size();
 433                                                 for (int k = 0; k < lookup.size(); k++) {
 434                                                         //is this descendant of j, and we didn't already add this as part of a larger grouping
 435                                                         if ((nodeToDescendants[j].count(lookup[k]->getGroup()) != 0) && (groupsAlreadyAdded.count(lookup[k]->getGroup()) == 0)) {
 436                                                                 subset.push_back(lookup[k]);
 437                                                                 groupsAlreadyAdded.insert(lookup[k]->getGroup());
 438                                                                 count++;
 439                                                         }
 440                                                         if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
 441                                                 }
 442
 443                                                 //if subset.size == 0 then the node was added as part of a larger grouping
 444                                                 if (subset.size() != 0) { groupings.push_back(subset); }
 445                                         }
 446                                 }
 447
 448                                 if (groupsAlreadyAdded.size() != lookup.size()) {  m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
 449
 450                                 indicatorValues = getValues(groupings);
 451
 452                         }else {
 453                                 vector< vector<SharedRAbundFloatVector*> > groupings;
 454
 455                                 //get nodes that will be a valid grouping
 456                                 //you are valid if you are not one of my descendants
 457                                 //AND your distToRoot is >= mine
 458                                 //AND you were not added as part of a larger grouping. Largest nodes are added first.
 459
 460                                 set<string> groupsAlreadyAdded;
 461                                 //create a grouping with my grouping
 462                                 vector<SharedRAbundFloatVector*> subset;
 463                                 int count = 0;
 464                                 int doneCount = nodeToDescendants[i].size();
 465                                 for (int k = 0; k < lookupFloat.size(); k++) {
 466                                         //is this descendant of i
 467                                         if ((nodeToDescendants[i].count(lookupFloat[k]->getGroup()) != 0)) {
 468                                                 subset.push_back(lookupFloat[k]);
 469                                                 groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
 470                                                 count++;
 471                                         }
 472                                         if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
 473                                 }
 474                                 if (subset.size() != 0) { groupings.push_back(subset); }
 475
 476                                 for (int j = (T->getNumNodes()-1); j >= 0; j--) {
 477                                         if ((descendantNodes[i].count(j) == 0) && (distToRoot[j] >= distToRoot[i])) {
 478                                                 vector<SharedRAbundFloatVector*> subset;
 479                                                 int count = 0;
 480                                                 int doneCount = nodeToDescendants[j].size();
 481                                                 for (int k = 0; k < lookupFloat.size(); k++) {
 482                                                         //is this descendant of j, and we didn't already add this as part of a larger grouping
 483                                                         if ((nodeToDescendants[j].count(lookupFloat[k]->getGroup()) != 0) && (groupsAlreadyAdded.count(lookupFloat[k]->getGroup()) == 0)) {
 484                                                                 subset.push_back(lookupFloat[k]);
 485                                                                 groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
 486                                                                 count++;
 487                                                         }
 488                                                         if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
 489                                                 }
 490
 491                                                 //if subset.size == 0 then the node was added as part of a larger grouping
 492                                                 if (subset.size() != 0) { groupings.push_back(subset); }
 493                                         }
 494                                 }
 495
 496                                 if (groupsAlreadyAdded.size() != lookupFloat.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
 497
 498                                 indicatorValues = getValues(groupings);
 499                         }
 500
 501                         if (m->control_pressed) { out.close(); return 0; }
 502
 503
 504                         /******************************************************/
 505                         //output indicator values to table form + label tree  //
 506                         /*****************************************************/
 507                         out << (i+1) << '\t';
 508                         for (int j = 0; j < indicatorValues.size(); j++) {
 509
 510                                 if (m->control_pressed) { out.close(); return 0; }
 511
 512                                 out << indicatorValues[j] << '\t';
 513                         }
 514                         out << endl;
 515
 516                         T->tree[i].setLabel((i+1));
 517
 518                 }
 519                 out.close();
 520
 521                 ofstream outTree;
 522                 m->openOutputFile(outputTreeFileName, outTree);
 523                 outputNames.push_back(outputTreeFileName); outputTypes["tree"].push_back(outputTreeFileName);
 524
 525                 T->print(outTree, "both");
 526                 outTree.close();
 527
 528                 return 0;
 529         }
 530         catch(exception& e) {
 531                 m->errorOut(e, "IndicatorCommand", "GetIndicatorSpecies");
 532                 exit(1);
 533         }
 534 }
 535 //**********************************************************************************************************************
 536 vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundFloatVector*> >& groupings){
 537         try {
 538                 vector<float> values;
 539
 540                 //for each otu
 541                 for (int i = 0; i < groupings[0][0]->getNumBins(); i++) {
 542
 543                         if (m->control_pressed) { return values; }
 544
 545                         vector<float> terms;
 546                         float AijDenominator = 0.0;
 547                         vector<float> Bij;
 548                         //get overall abundance of each grouping
 549                         for (int j = 0; j < groupings.size(); j++) {
 550
 551                                 float totalAbund = 0;
 552                                 int numNotZero = 0;
 553                                 for (int k = 0; k < groupings[j].size(); k++) {
 554                                         totalAbund += groupings[j][k]->getAbundance(i);
 555                                         if (groupings[j][k]->getAbundance(i) != 0) { numNotZero++; }
 556                                 }
 557
 558                                 float Aij = (totalAbund / (float) groupings[j].size());
 559                                 terms.push_back(Aij);
 560
 561                                 //percentage of sites represented
 562                                 Bij.push_back(numNotZero / (float) groupings[j].size());
 563
 564                                 AijDenominator += Aij;
 565                         }
 566
 567                         float maxIndVal = 0.0;
 568                         for (int j = 0; j < terms.size(); j++) {
 569                                 float thisAij = (terms[j] / AijDenominator);
 570                                 float thisValue = thisAij * Bij[j] * 100.0;
 571
 572                                 //save largest
 573                                 if (thisValue > maxIndVal) { maxIndVal = thisValue; }
 574                         }
 575
 576                         values.push_back(maxIndVal);
 577                 }
 578
 579                 return values;
 580         }
 581         catch(exception& e) {
 582                 m->errorOut(e, "IndicatorCommand", "getValues");
 583                 exit(1);
 584         }
 585 }
 586 //**********************************************************************************************************************
 587 //same as above, just data type difference
 588 vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundVector*> >& groupings){
 589         try {
 590                 vector<float> values;
 591
 592         /*for (int j = 0; j < groupings.size(); j++) {
 593                 cout << "grouping " << j << endl;
 594                 for (int k = 0; k < groupings[j].size(); k++) {
 595                         cout << groupings[j][k]->getGroup() << endl;
 596                 }
 597         }*/
 598                 //for each otu
 599                 for (int i = 0; i < groupings[0][0]->getNumBins(); i++) {
 600                         vector<float> terms;
 601                         float AijDenominator = 0.0;
 602                         vector<float> Bij;
 603                         //get overall abundance of each grouping
 604                         for (int j = 0; j < groupings.size(); j++) {
 605
 606                                 int totalAbund = 0.0;
 607                                 int numNotZero = 0;
 608                                 for (int k = 0; k < groupings[j].size(); k++) {
 609                                         totalAbund += groupings[j][k]->getAbundance(i);
 610                                         if (groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
 611
 612                                 }
 613
 614                                 float Aij = (totalAbund / (float) groupings[j].size());
 615                                 terms.push_back(Aij);
 616
 617                                 //percentage of sites represented
 618                                 Bij.push_back(numNotZero / (float) groupings[j].size());
 619
 620                                 AijDenominator += Aij;
 621                         }
 622
 623                         float maxIndVal = 0.0;
 624                         for (int j = 0; j < terms.size(); j++) {
 625                                 float thisAij = (terms[j] / AijDenominator);
 626                                 float thisValue = thisAij * Bij[j] * 100.0;
 627
 628                                 //save largest
 629                                 if (thisValue > maxIndVal) { maxIndVal = thisValue; }
 630                         }
 631
 632                         values.push_back(maxIndVal);
 633                 }
 634
 635                 return values;
 636         }
 637         catch(exception& e) {
 638                 m->errorOut(e, "IndicatorCommand", "getValues");
 639                 exit(1);
 640         }
 641 }
 642 //**********************************************************************************************************************
 643 //you need the distances to root to decide groupings
 644 //this will also set branch lengths if the tree does not include them
 645 map<int, float> IndicatorCommand::getDistToRoot(Tree*& T){
 646         try {
 647                 map<int, float> dists;
 648
 649                 bool hasBranchLengths = false;
 650                 for (int i = 0; i < T->getNumNodes(); i++) {
 651                         if (T->tree[i].getBranchLength() > 0.0) {  hasBranchLengths = true; break; }
 652                 }
 653
 654                 //set branchlengths if needed
 655                 if (!hasBranchLengths) {
 656                         for (int i = 0; i < T->getNumNodes(); i++) {
 657
 658                                 int lc = T->tree[i].getLChild();
 659                                 int rc = T->tree[i].getRChild();
 660
 661                                 if (lc == -1) { // you are a leaf
 662                                         //if you are a leaf set you priliminary length to 1.0, this may adjust later
 663                                         T->tree[i].setBranchLength(1.0);
 664                                         dists[i] = 1.0;
 665                                 }else{ // you are an internal node
 666                                         //look at your children's length to leaf
 667                                         float ldist = dists[lc];
 668                                         float rdist = dists[rc];
 669
 670                                         float greater = ldist;
 671                                         if (rdist > greater) { greater = rdist; dists[i] = ldist + 1.0;}
 672                                         else { dists[i] = rdist + 1.0; }
 673
 674
 675                                         //branch length = difference + 1
 676                                         T->tree[lc].setBranchLength((abs(ldist-greater) + 1.0));
 677                                         T->tree[rc].setBranchLength((abs(rdist-greater) + 1.0));
 678                                 }
 679                         }
 680                 }
 681
 682                 dists.clear();
 683
 684                 for (int i = 0; i < T->getNumNodes(); i++) {
 685
 686                         double sum = 0.0;
 687                         int index = i;
 688
 689                         while(T->tree[index].getParent() != -1){
 690                                 if (T->tree[index].getBranchLength() != -1) {
 691                                         sum += abs(T->tree[index].getBranchLength());
 692                                 }
 693                                 index = T->tree[index].getParent();
 694                         }
 695
 696                         dists[i] = sum;
 697                 }
 698
 699                 return dists;
 700         }
 701         catch(exception& e) {
 702                 m->errorOut(e, "IndicatorCommand", "getLengthToLeaf");
 703                 exit(1);
 704         }
 705 }
 706 //**********************************************************************************************************************
 707 set<string> IndicatorCommand::getDescendantList(Tree*& T, int i, map<int, set<string> > descendants, map<int, set<int> >& nodes){
 708         try {
 709                 set<string> names;
 710
 711                 set<string>::iterator it;
 712
 713                 int lc = T->tree[i].getLChild();
 714                 int rc = T->tree[i].getRChild();
 715
 716                 if (lc == -1) { //you are a leaf your only descendant is yourself
 717                         set<int> temp; temp.insert(i);
 718                         nodes[i] = temp;
 719
 720                         if (designfile == "") {
 721                                 names.insert(T->tree[i].getName());
 722                         }else {
 723                                 vector<string> myGroup; myGroup.push_back(T->tree[i].getName());
 724                                 vector<string> myReps = designMap->getNamesSeqs(myGroup);
 725                                 for (int k = 0; k < myReps.size(); k++) {
 726                                         names.insert(myReps[k]);
 727                                 }
 728                         }
 729
 730                 }else{ //your descedants are the combination of your childrens descendants
 731                         names = descendants[lc];
 732                         nodes[i] = nodes[lc];
 733                         for (it = descendants[rc].begin(); it != descendants[rc].end(); it++) {
 734                                 names.insert(*it);
 735                         }
 736                         for (set<int>::iterator itNum = nodes[rc].begin(); itNum != nodes[rc].end(); itNum++) {
 737                                 nodes[i].insert(*itNum);
 738                         }
 739                         //you are your own descendant
 740                         nodes[i].insert(i);
 741                 }
 742
 743                 return names;
 744         }
 745         catch(exception& e) {
 746                 m->errorOut(e, "IndicatorCommand", "getDescendantList");
 747                 exit(1);
 748         }
 749 }
 750 //**********************************************************************************************************************
 751 int IndicatorCommand::getShared(){
 752         try {
 753                 InputData* input = new InputData(sharedfile, "sharedfile");
 754                 lookup = input->getSharedRAbundVectors();
 755                 string lastLabel = lookup[0]->getLabel();
 756
 757                 if (label == "") { label = lastLabel; delete input; return 0; }
 758
 759                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 760                 set<string> labels; labels.insert(label);
 761                 set<string> processedLabels;
 762                 set<string> userLabels = labels;
 763
 764                 //as long as you are not at the end of the file or done wih the lines you want
 765                 while((lookup[0] != NULL) && (userLabels.size() != 0)) {
 766                         if (m->control_pressed) {  delete input; return 0;  }
 767
 768                         if(labels.count(lookup[0]->getLabel()) == 1){
 769                                 processedLabels.insert(lookup[0]->getLabel());
 770                                 userLabels.erase(lookup[0]->getLabel());
 771                                 break;
 772                         }
 773
 774                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 775                                 string saveLabel = lookup[0]->getLabel();
 776
 777                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 778                                 lookup = input->getSharedRAbundVectors(lastLabel);
 779
 780                                 processedLabels.insert(lookup[0]->getLabel());
 781                                 userLabels.erase(lookup[0]->getLabel());
 782
 783                                 //restore real lastlabel to save below
 784                                 lookup[0]->setLabel(saveLabel);
 785                                 break;
 786                         }
 787
 788                         lastLabel = lookup[0]->getLabel();
 789
 790                         //get next line to process
 791                         //prevent memory leak
 792                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 793                         lookup = input->getSharedRAbundVectors();
 794                 }
 795
 796
 797                 if (m->control_pressed) { delete input; return 0;  }
 798
 799                 //output error messages about any remaining user labels
 800                 set<string>::iterator it;
 801                 bool needToRun = false;
 802                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 803                         m->mothurOut("Your file does not include the label " + *it);
 804                         if (processedLabels.count(lastLabel) != 1) {
 805                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 806                                 needToRun = true;
 807                         }else {
 808                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 809                         }
 810                 }
 811
 812                 //run last label if you need to
 813                 if (needToRun == true)  {
 814                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i];       } }
 815                         lookup = input->getSharedRAbundVectors(lastLabel);
 816                 }
 817
 818                 delete input;
 819                 return 0;
 820         }
 821         catch(exception& e) {
 822                 m->errorOut(e, "IndicatorCommand", "getShared");
 823                 exit(1);
 824         }
 825 }
 826 //**********************************************************************************************************************
 827 int IndicatorCommand::getSharedFloat(){
 828         try {
 829                 InputData* input = new InputData(relabundfile, "relabund");
 830                 lookupFloat = input->getSharedRAbundFloatVectors();
 831                 string lastLabel = lookupFloat[0]->getLabel();
 832
 833                 if (label == "") { label = lastLabel; delete input; return 0; }
 834
 835                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 836                 set<string> labels; labels.insert(label);
 837                 set<string> processedLabels;
 838                 set<string> userLabels = labels;
 839
 840                 //as long as you are not at the end of the file or done wih the lines you want
 841                 while((lookupFloat[0] != NULL) && (userLabels.size() != 0)) {
 842
 843                         if (m->control_pressed) {  delete input; return 0;  }
 844
 845                         if(labels.count(lookupFloat[0]->getLabel()) == 1){
 846                                 processedLabels.insert(lookupFloat[0]->getLabel());
 847                                 userLabels.erase(lookupFloat[0]->getLabel());
 848                                 break;
 849                         }
 850
 851                         if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 852                                 string saveLabel = lookupFloat[0]->getLabel();
 853
 854                                 for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 855                                 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 856
 857                                 processedLabels.insert(lookupFloat[0]->getLabel());
 858                                 userLabels.erase(lookupFloat[0]->getLabel());
 859
 860                                 //restore real lastlabel to save below
 861                                 lookupFloat[0]->setLabel(saveLabel);
 862                                 break;
 863                         }
 864
 865                         lastLabel = lookupFloat[0]->getLabel();
 866
 867                         //get next line to process
 868                         //prevent memory leak
 869                         for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 870                         lookupFloat = input->getSharedRAbundFloatVectors();
 871                 }
 872
 873
 874                 if (m->control_pressed) { delete input; return 0;  }
 875
 876                 //output error messages about any remaining user labels
 877                 set<string>::iterator it;
 878                 bool needToRun = false;
 879                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 880                         m->mothurOut("Your file does not include the label " + *it);
 881                         if (processedLabels.count(lastLabel) != 1) {
 882                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 883                                 needToRun = true;
 884                         }else {
 885                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 886                         }
 887                 }
 888
 889                 //run last label if you need to
 890                 if (needToRun == true)  {
 891                         for (int i = 0; i < lookupFloat.size(); i++) {  if (lookupFloat[i] != NULL) {   delete lookupFloat[i];  } }
 892                         lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 893                 }
 894
 895                 delete input;
 896                 return 0;
 897         }
 898         catch(exception& e) {
 899                 m->errorOut(e, "IndicatorCommand", "getShared");
 900         exit(1);
 901         }
 902 }
 903 /*****************************************************************/
 904
 905