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