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