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