indicatorcommand.cpp

   1 /*
   2  *  indicatorcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 11/12/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "indicatorcommand.h"
  11 #include "sharedutilities.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> IndicatorCommand::getValidParameters(){
  15         try {
  16                 string Array[] =  {"tree","shared","relabund","design","label","groups","outputdir","inputdir"};
  17                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "IndicatorCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 vector<string> IndicatorCommand::getRequiredParameters(){
  27         try {
  28                 string Array[] =  {"tree"};
  29                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  30                 return myArray;
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "IndicatorCommand", "getRequiredParameters");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 IndicatorCommand::IndicatorCommand(){
  39         try {
  40                 abort = true;
  41                 //initialize outputTypes
  42                 vector<string> tempOutNames;
  43                 outputTypes["tree"] = tempOutNames;
  44                 outputTypes["summary"] = tempOutNames;
  45         }
  46         catch(exception& e) {
  47                 m->errorOut(e, "IndicatorCommand", "IndicatorCommand");
  48                 exit(1);
  49         }
  50 }
  51
  52 //**********************************************************************************************************************
  53 vector<string> IndicatorCommand::getRequiredFiles(){
  54         try {
  55                 vector<string> myArray;
  56                 return myArray;
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "IndicatorCommand", "getRequiredFiles");
  60                 exit(1);
  61         }
  62 }
  63 //**********************************************************************************************************************
  64 IndicatorCommand::IndicatorCommand(string option)  {
  65         try {
  66                 globaldata = GlobalData::getInstance();
  67                 abort = false;
  68
  69                 //allow user to run help
  70                 if(option == "help") { help(); abort = true; }
  71
  72                 else {
  73                         //valid paramters for this command
  74                         string Array[] =  {"tree","shared","design","relabund","groups","label","outputdir","inputdir"};
  75                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  76
  77                         OptionParser parser(option);
  78                         map<string, string> parameters = parser.getParameters();
  79
  80                         ValidParameters validParameter;
  81                         map<string, string>::iterator it;
  82
  83                         //check to make sure all parameters are valid for command
  84                         for (it = parameters.begin(); it != parameters.end(); it++) {
  85                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  86                         }
  87
  88                         globaldata->newRead();
  89
  90                         vector<string> tempOutNames;
  91                         outputTypes["tree"] = tempOutNames;
  92                         outputTypes["summary"] = tempOutNames;
  93
  94                         //if the user changes the input directory command factory will send this info to us in the output parameter
  95                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  96                         if (inputDir == "not found"){   inputDir = "";          }
  97                         else {
  98                                 string path;
  99                                 it = parameters.find("tree");
 100                                 //user has given a template file
 101                                 if(it != parameters.end()){
 102                                         path = m->hasPath(it->second);
 103                                         //if the user has not given a path then, add inputdir. else leave path alone.
 104                                         if (path == "") {       parameters["tree"] = inputDir + it->second;             }
 105                                 }
 106
 107                                 it = parameters.find("shared");
 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["shared"] = inputDir + it->second;           }
 113                                 }
 114
 115                                 it = parameters.find("relabund");
 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["relabund"] = inputDir + it->second;         }
 121                                 }
 122
 123                                 it = parameters.find("design");
 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["design"] = inputDir + it->second;           }
 129                                 }
 130                         }
 131
 132                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 133
 134                         //check for required parameters
 135                         treefile = validParameter.validFile(parameters, "tree", true);
 136                         if (treefile == "not open") { abort = true; }
 137                         else if (treefile == "not found") { treefile = ""; m->mothurOut("tree is a required parameter for the indicator command."); m->mothurOutEndLine(); abort = true;  }
 138                         else {  globaldata->setTreeFile(treefile);  globaldata->setFormat("tree");      }
 139
 140                         sharedfile = validParameter.validFile(parameters, "shared", true);
 141                         if (sharedfile == "not open") { abort = true; }
 142                         else if (sharedfile == "not found") { sharedfile = ""; }
 143                         else { inputFileName = sharedfile; }
 144
 145                         relabundfile = validParameter.validFile(parameters, "relabund", true);
 146                         if (relabundfile == "not open") { abort = true; }
 147                         else if (relabundfile == "not found") { relabundfile = ""; }
 148                         else { inputFileName = relabundfile; }
 149
 150                         designfile = validParameter.validFile(parameters, "design", true);
 151                         if (designfile == "not open") { abort = true; }
 152                         else if (designfile == "not found") { designfile = ""; }
 153
 154                         groups = validParameter.validFile(parameters, "groups", false);
 155                         if (groups == "not found") { groups = "";  Groups.push_back("all"); }
 156                         else { m->splitAtDash(groups, Groups);  }
 157                         globaldata->Groups = Groups;
 158
 159                         label = validParameter.validFile(parameters, "label", false);
 160                         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=""; }
 161
 162                         if ((relabundfile == "") && (sharedfile == "")) { m->mothurOut("You must provide either a shared or relabund file."); m->mothurOutEndLine(); abort = true;  }
 163
 164                         if ((relabundfile != "") && (sharedfile != "")) { m->mothurOut("You may not use both a shared and relabund file."); m->mothurOutEndLine(); abort = true;  }
 165
 166                 }
 167         }
 168         catch(exception& e) {
 169                 m->errorOut(e, "IndicatorCommand", "IndicatorCommand");
 170                 exit(1);
 171         }
 172 }
 173 //**********************************************************************************************************************
 174
 175 void IndicatorCommand::help(){
 176         try {
 177                 m->mothurOut("The indicator command reads a shared or relabund file and a tree file, and outputs a .indicator.tre and .indicator.summary file. \n");
 178                 m->mothurOut("The new tree contains labels at each internal node.  The label is the node number so you can relate the tree to the summary file.\n");
 179                 m->mothurOut("The summary file lists the indicator value for each OTU for each node.\n");
 180                 m->mothurOut("The indicator command parameters are tree, groups, shared, relabund, design and label. The tree parameter is required as well as either shared or relabund.\n");
 181                 m->mothurOut("The design parameter allows you to provide a design file to relate the tree to the shared or relabund file.\n");
 182                 m->mothurOut("The groups parameter allows you to specify which of the groups in your shared or relabund you would like analyzed, or if you provide a design file the groups in your design file.  The groups may be entered separated by dashes.\n");
 183                 m->mothurOut("The label parameter indicates at what distance your tree relates to the shared or relabund.\n");
 184                 m->mothurOut("The indicator command should be used in the following format: indicator(tree=test.tre, shared=test.shared, label=0.03)\n");
 185                 m->mothurOut("Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n");
 186         }
 187         catch(exception& e) {
 188                 m->errorOut(e, "IndicatorCommand", "help");
 189                 exit(1);
 190         }
 191 }
 192
 193 //**********************************************************************************************************************
 194
 195 IndicatorCommand::~IndicatorCommand(){}
 196
 197 //**********************************************************************************************************************
 198
 199 int IndicatorCommand::execute(){
 200         try {
 201
 202                 if (abort == true) { return 0; }
 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                         globaldata->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 != "") { globaldata->Groups = Groups; }
 233
 234                 /***************************************************/
 235                 //    reading tree info                                                    //
 236                 /***************************************************/
 237                 string groupfile = "";
 238                 Tree* tree = new Tree(treefile); delete tree;  //extracts names from tree to make faked out groupmap
 239
 240                 globaldata->setGroupFile(groupfile);
 241                 treeMap = new TreeMap();
 242                 bool mismatch = false;
 243
 244                 for (int i = 0; i < globaldata->Treenames.size(); i++) {
 245                         //sanity check - is this a group that is not in the sharedfile?
 246                         if (designfile == "") {
 247                                 if (!(m->inUsersGroups(globaldata->Treenames[i], globaldata->gGroupmap->namesOfGroups))) {
 248                                         m->mothurOut("[ERROR]: " + globaldata->Treenames[i] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
 249                                         mismatch = true;
 250                                 }
 251                                 treeMap->addSeq(globaldata->Treenames[i], "Group1");
 252                         }else{
 253                                 vector<string> myGroups; myGroups.push_back(globaldata->Treenames[i]);
 254                                 vector<string> myNames = designMap->getNamesSeqs(myGroups);
 255
 256                                 for(int k = 0; k < myNames.size(); k++) {
 257                                         if (!(m->inUsersGroups(myNames[k], globaldata->gGroupmap->namesOfGroups))) {
 258                                                 m->mothurOut("[ERROR]: " + myNames[k] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
 259                                                 mismatch = true;
 260                                         }
 261                                 }
 262                                 treeMap->addSeq(globaldata->Treenames[i], "Group1");
 263                         }
 264                 }
 265
 266                 if ((designfile != "") && (globaldata->Treenames.size() != Groups.size())) { m->mothurOut("[ERROR]: You design file does not match your tree, aborting."); m->mothurOutEndLine(); mismatch = true; }
 267
 268                 if (mismatch) { //cleanup and exit
 269                         if (designfile != "") { delete designMap; }
 270                         if (sharedfile != "") {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } }
 271                         else { for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } }
 272                         delete treeMap;
 273                         return 0;
 274                 }
 275
 276                 globaldata->gTreemap = treeMap;
 277
 278                 read = new ReadNewickTree(treefile);
 279                 int readOk = read->read();
 280
 281                 if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); globaldata->gTree.clear(); delete globaldata->gTreemap; delete read; return 0; }
 282
 283                 vector<Tree*> T = globaldata->gTree;
 284
 285                 delete read;
 286
 287                 if (m->control_pressed) {
 288                         if (designfile != "") { delete designMap; }
 289                         if (sharedfile != "") {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } }
 290                         else { for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } }
 291                         for (int i = 0; i < T.size(); i++) {  delete T[i];  } globaldata->gTree.clear(); delete globaldata->gTreemap; return 0;
 292                 }
 293
 294                 T[0]->assembleTree();
 295
 296                 /***************************************************/
 297                 //    create ouptut tree - respecting pickedGroups //
 298                 /***************************************************/
 299                 Tree* outputTree = new Tree(globaldata->Groups.size());
 300
 301                 outputTree->getSubTree(T[0], globaldata->Groups);
 302                 outputTree->assembleTree();
 303
 304                 //no longer need original tree, we have output tree to use and label
 305                 for (int i = 0; i < T.size(); i++) {  delete T[i];  } globaldata->gTree.clear();
 306
 307
 308                 if (m->control_pressed) {
 309                         if (designfile != "") { delete designMap; }
 310                         if (sharedfile != "") {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } }
 311                         else { for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } }
 312                         delete outputTree; delete globaldata->gTreemap;  return 0;
 313                 }
 314
 315                 /***************************************************/
 316                 //              get indicator species values                       //
 317                 /***************************************************/
 318                 GetIndicatorSpecies(outputTree);
 319
 320                 if (designfile != "") { delete designMap; }
 321
 322                 if (m->control_pressed) {
 323                         if (sharedfile != "") {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } }
 324                         else { for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } }
 325                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 326                         delete outputTree; delete globaldata->gTreemap;  return 0;
 327                 }
 328
 329                 m->mothurOutEndLine();
 330                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 331                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 332                 m->mothurOutEndLine();
 333
 334                 return 0;
 335         }
 336         catch(exception& e) {
 337                 m->errorOut(e, "IndicatorCommand", "execute");
 338                 exit(1);
 339         }
 340 }
 341 //**********************************************************************************************************************
 342 //traverse tree finding indicator species values for each otu at each node
 343 //label node with otu number that has highest indicator value
 344 //report all otu values to file
 345 int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
 346         try {
 347
 348                 string thisOutputDir = outputDir;
 349                 if (outputDir == "") {  thisOutputDir += m->hasPath(inputFileName);  }
 350                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
 351                 outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
 352
 353                 ofstream out;
 354                 m->openOutputFile(outputFileName, out);
 355                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 356
 357                 int numBins = 0;
 358                 if (sharedfile != "") { numBins = lookup[0]->getNumBins(); }
 359                 else { numBins = lookupFloat[0]->getNumBins(); }
 360
 361                 //print headings
 362                 out << "TreeNode\t";
 363                 for (int i = 0; i < numBins; i++) { out << "OTU-" << (i+1) << '\t'; }
 364                 out << endl;
 365
 366                 string treeOutputDir = outputDir;
 367                 if (outputDir == "") {  treeOutputDir += m->hasPath(treefile);  }
 368                 string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "indicator.tre";
 369
 370
 371                 //create a map from tree node index to names of descendants, save time later to know which sharedRabund you need
 372                 map<int, set<string> > nodeToDescendants;
 373                 map<int, set<int> > descendantNodes;
 374                 for (int i = 0; i < T->getNumNodes(); i++) {
 375                         if (m->control_pressed) { return 0; }
 376
 377                         nodeToDescendants[i] = getDescendantList(T, i, nodeToDescendants, descendantNodes);
 378                 }
 379
 380                 //you need the distances to leaf to decide grouping below
 381                 //this will also set branch lengths if the tree does not include them
 382                 map<int, float> distToRoot = getDistToRoot(T);
 383
 384                 //for each node
 385                 for (int i = T->getNumLeaves(); i < T->getNumNodes(); i++) {
 386
 387                         if (m->control_pressed) { out.close(); return 0; }
 388
 389                         /*****************************************************/
 390                         //create vectors containing rabund info                          //
 391                         /*****************************************************/
 392
 393                         vector<float> indicatorValues; //size of numBins
 394
 395                         if (sharedfile != "") {
 396                                 vector< vector<SharedRAbundVector*> > groupings;
 397
 398                                 //get nodes that will be a valid grouping
 399                                 //you are valid if you are not one of my descendants
 400                                 //AND your distToRoot is >= mine
 401                                 //AND you were not added as part of a larger grouping. Largest nodes are added first.
 402
 403                                 set<string> groupsAlreadyAdded;
 404                                 //create a grouping with my grouping
 405                                 vector<SharedRAbundVector*> subset;
 406                                 int count = 0;
 407                                 int doneCount = nodeToDescendants[i].size();
 408                                 for (int k = 0; k < lookup.size(); k++) {
 409                                         //is this descendant of i
 410                                         if ((nodeToDescendants[i].count(lookup[k]->getGroup()) != 0)) {
 411                                                 subset.push_back(lookup[k]);
 412                                                 groupsAlreadyAdded.insert(lookup[k]->getGroup());
 413                                                 count++;
 414                                         }
 415                                         if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
 416                                 }
 417                                 if (subset.size() != 0) { groupings.push_back(subset); }
 418
 419
 420                                 for (int j = (T->getNumNodes()-1); j >= 0; j--) {
 421
 422
 423                                         if ((descendantNodes[i].count(j) == 0) && (distToRoot[j] >= distToRoot[i])) {
 424                                                 vector<SharedRAbundVector*> subset;
 425                                                 int count = 0;
 426                                                 int doneCount = nodeToDescendants[j].size();
 427                                                 for (int k = 0; k < lookup.size(); k++) {
 428                                                         //is this descendant of j, and we didn't already add this as part of a larger grouping
 429                                                         if ((nodeToDescendants[j].count(lookup[k]->getGroup()) != 0) && (groupsAlreadyAdded.count(lookup[k]->getGroup()) == 0)) {
 430                                                                 subset.push_back(lookup[k]);
 431                                                                 groupsAlreadyAdded.insert(lookup[k]->getGroup());
 432                                                                 count++;
 433                                                         }
 434                                                         if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
 435                                                 }
 436
 437                                                 //if subset.size == 0 then the node was added as part of a larger grouping
 438                                                 if (subset.size() != 0) { groupings.push_back(subset); }
 439                                         }
 440                                 }
 441
 442                                 if (groupsAlreadyAdded.size() != lookup.size()) {  m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
 443
 444                                 indicatorValues = getValues(groupings);
 445
 446                         }else {
 447                                 vector< vector<SharedRAbundFloatVector*> > groupings;
 448
 449                                 //get nodes that will be a valid grouping
 450                                 //you are valid if you are not one of my descendants
 451                                 //AND your distToRoot is >= mine
 452                                 //AND you were not added as part of a larger grouping. Largest nodes are added first.
 453
 454                                 set<string> groupsAlreadyAdded;
 455                                 //create a grouping with my grouping
 456                                 vector<SharedRAbundFloatVector*> subset;
 457                                 int count = 0;
 458                                 int doneCount = nodeToDescendants[i].size();
 459                                 for (int k = 0; k < lookupFloat.size(); k++) {
 460                                         //is this descendant of i
 461                                         if ((nodeToDescendants[i].count(lookupFloat[k]->getGroup()) != 0)) {
 462                                                 subset.push_back(lookupFloat[k]);
 463                                                 groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
 464                                                 count++;
 465                                         }
 466                                         if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
 467                                 }
 468                                 if (subset.size() != 0) { groupings.push_back(subset); }
 469
 470                                 for (int j = (T->getNumNodes()-1); j >= 0; j--) {
 471                                         if ((descendantNodes[i].count(j) == 0) && (distToRoot[j] >= distToRoot[i])) {
 472                                                 vector<SharedRAbundFloatVector*> subset;
 473                                                 int count = 0;
 474                                                 int doneCount = nodeToDescendants[j].size();
 475                                                 for (int k = 0; k < lookupFloat.size(); k++) {
 476                                                         //is this descendant of j, and we didn't already add this as part of a larger grouping
 477                                                         if ((nodeToDescendants[j].count(lookupFloat[k]->getGroup()) != 0) && (groupsAlreadyAdded.count(lookupFloat[k]->getGroup()) == 0)) {
 478                                                                 subset.push_back(lookupFloat[k]);
 479                                                                 groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
 480                                                                 count++;
 481                                                         }
 482                                                         if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
 483                                                 }
 484
 485                                                 //if subset.size == 0 then the node was added as part of a larger grouping
 486                                                 if (subset.size() != 0) { groupings.push_back(subset); }
 487                                         }
 488                                 }
 489
 490                                 if (groupsAlreadyAdded.size() != lookupFloat.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
 491
 492                                 indicatorValues = getValues(groupings);
 493                         }
 494
 495                         if (m->control_pressed) { out.close(); return 0; }
 496
 497
 498                         /******************************************************/
 499                         //output indicator values to table form + label tree  //
 500                         /*****************************************************/
 501                         out << (i+1) << '\t';
 502                         for (int j = 0; j < indicatorValues.size(); j++) {
 503
 504                                 if (m->control_pressed) { out.close(); return 0; }
 505
 506                                 out << indicatorValues[j] << '\t';
 507                         }
 508                         out << endl;
 509
 510                         T->tree[i].setLabel((i+1));
 511
 512                 }
 513                 out.close();
 514
 515                 ofstream outTree;
 516                 m->openOutputFile(outputTreeFileName, outTree);
 517                 outputNames.push_back(outputTreeFileName); outputTypes["tree"].push_back(outputTreeFileName);
 518
 519                 T->print(outTree, "both");
 520                 outTree.close();
 521
 522                 return 0;
 523         }
 524         catch(exception& e) {
 525                 m->errorOut(e, "IndicatorCommand", "GetIndicatorSpecies");
 526                 exit(1);
 527         }
 528 }
 529 //**********************************************************************************************************************
 530 vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundFloatVector*> >& groupings){
 531         try {
 532                 vector<float> values;
 533
 534                 //for each otu
 535                 for (int i = 0; i < groupings[0][0]->getNumBins(); i++) {
 536
 537                         if (m->control_pressed) { return values; }
 538
 539                         vector<float> terms;
 540                         float AijDenominator = 0.0;
 541                         vector<float> Bij;
 542                         //get overall abundance of each grouping
 543                         for (int j = 0; j < groupings.size(); j++) {
 544
 545                                 float totalAbund = 0;
 546                                 int numNotZero = 0;
 547                                 for (int k = 0; k < groupings[j].size(); k++) {
 548                                         totalAbund += groupings[j][k]->getAbundance(i);
 549                                         if (groupings[j][k]->getAbundance(i) != 0) { numNotZero++; }
 550                                 }
 551
 552                                 float Aij = (totalAbund / (float) groupings[j].size());
 553                                 terms.push_back(Aij);
 554
 555                                 //percentage of sites represented
 556                                 Bij.push_back(numNotZero / (float) groupings[j].size());
 557
 558                                 AijDenominator += Aij;
 559                         }
 560
 561                         float maxIndVal = 0.0;
 562                         for (int j = 0; j < terms.size(); j++) {
 563                                 float thisAij = (terms[j] / AijDenominator);
 564                                 float thisValue = thisAij * Bij[j] * 100.0;
 565
 566                                 //save largest
 567                                 if (thisValue > maxIndVal) { maxIndVal = thisValue; }
 568                         }
 569
 570                         values.push_back(maxIndVal);
 571                 }
 572
 573                 return values;
 574         }
 575         catch(exception& e) {
 576                 m->errorOut(e, "IndicatorCommand", "getValues");
 577                 exit(1);
 578         }
 579 }
 580 //**********************************************************************************************************************
 581 //same as above, just data type difference
 582 vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundVector*> >& groupings){
 583         try {
 584                 vector<float> values;
 585
 586         /*for (int j = 0; j < groupings.size(); j++) {
 587                 cout << "grouping " << j << endl;
 588                 for (int k = 0; k < groupings[j].size(); k++) {
 589                         cout << groupings[j][k]->getGroup() << endl;
 590                 }
 591         }*/
 592                 //for each otu
 593                 for (int i = 0; i < groupings[0][0]->getNumBins(); i++) {
 594                         vector<float> terms;
 595                         float AijDenominator = 0.0;
 596                         vector<float> Bij;
 597                         //get overall abundance of each grouping
 598                         for (int j = 0; j < groupings.size(); j++) {
 599
 600                                 int totalAbund = 0.0;
 601                                 int numNotZero = 0;
 602                                 for (int k = 0; k < groupings[j].size(); k++) {
 603                                         totalAbund += groupings[j][k]->getAbundance(i);
 604                                         if (groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
 605
 606                                 }
 607
 608                                 float Aij = (totalAbund / (float) groupings[j].size());
 609                                 terms.push_back(Aij);
 610
 611                                 //percentage of sites represented
 612                                 Bij.push_back(numNotZero / (float) groupings[j].size());
 613
 614                                 AijDenominator += Aij;
 615                         }
 616
 617                         float maxIndVal = 0.0;
 618                         for (int j = 0; j < terms.size(); j++) {
 619                                 float thisAij = (terms[j] / AijDenominator);
 620                                 float thisValue = thisAij * Bij[j] * 100.0;
 621
 622                                 //save largest
 623                                 if (thisValue > maxIndVal) { maxIndVal = thisValue; }
 624                         }
 625
 626                         values.push_back(maxIndVal);
 627                 }
 628
 629                 return values;
 630         }
 631         catch(exception& e) {
 632                 m->errorOut(e, "IndicatorCommand", "getValues");
 633                 exit(1);
 634         }
 635 }
 636 //**********************************************************************************************************************
 637 //you need the distances to root to decide groupings
 638 //this will also set branch lengths if the tree does not include them
 639 map<int, float> IndicatorCommand::getDistToRoot(Tree*& T){
 640         try {
 641                 map<int, float> dists;
 642
 643                 bool hasBranchLengths = false;
 644                 for (int i = 0; i < T->getNumNodes(); i++) {
 645                         if (T->tree[i].getBranchLength() > 0.0) {  hasBranchLengths = true; break; }
 646                 }
 647
 648                 //set branchlengths if needed
 649                 if (!hasBranchLengths) {
 650                         for (int i = 0; i < T->getNumNodes(); i++) {
 651
 652                                 int lc = T->tree[i].getLChild();
 653                                 int rc = T->tree[i].getRChild();
 654
 655                                 if (lc == -1) { // you are a leaf
 656                                         //if you are a leaf set you priliminary length to 1.0, this may adjust later
 657                                         T->tree[i].setBranchLength(1.0);
 658                                         dists[i] = 1.0;
 659                                 }else{ // you are an internal node
 660                                         //look at your children's length to leaf
 661                                         float ldist = dists[lc];
 662                                         float rdist = dists[rc];
 663
 664                                         float greater = ldist;
 665                                         if (rdist > greater) { greater = rdist; dists[i] = ldist + 1.0;}
 666                                         else { dists[i] = rdist + 1.0; }
 667
 668
 669                                         //branch length = difference + 1
 670                                         T->tree[lc].setBranchLength((abs(ldist-greater) + 1.0));
 671                                         T->tree[rc].setBranchLength((abs(rdist-greater) + 1.0));
 672                                 }
 673                         }
 674                 }
 675
 676                 dists.clear();
 677
 678                 for (int i = 0; i < T->getNumNodes(); i++) {
 679
 680                         double sum = 0.0;
 681                         int index = i;
 682
 683                         while(T->tree[index].getParent() != -1){
 684                                 if (T->tree[index].getBranchLength() != -1) {
 685                                         sum += abs(T->tree[index].getBranchLength());
 686                                 }
 687                                 index = T->tree[index].getParent();
 688                         }
 689
 690                         dists[i] = sum;
 691                 }
 692
 693                 return dists;
 694         }
 695         catch(exception& e) {
 696                 m->errorOut(e, "IndicatorCommand", "getLengthToLeaf");
 697                 exit(1);
 698         }
 699 }
 700 //**********************************************************************************************************************
 701 set<string> IndicatorCommand::getDescendantList(Tree*& T, int i, map<int, set<string> > descendants, map<int, set<int> >& nodes){
 702         try {
 703                 set<string> names;
 704
 705                 set<string>::iterator it;
 706
 707                 int lc = T->tree[i].getLChild();
 708                 int rc = T->tree[i].getRChild();
 709
 710                 if (lc == -1) { //you are a leaf your only descendant is yourself
 711                         set<int> temp; temp.insert(i);
 712                         nodes[i] = temp;
 713
 714                         if (designfile == "") {
 715                                 names.insert(T->tree[i].getName());
 716                         }else {
 717                                 vector<string> myGroup; myGroup.push_back(T->tree[i].getName());
 718                                 vector<string> myReps = designMap->getNamesSeqs(myGroup);
 719                                 for (int k = 0; k < myReps.size(); k++) {
 720                                         names.insert(myReps[k]);
 721                                 }
 722                         }
 723
 724                 }else{ //your descedants are the combination of your childrens descendants
 725                         names = descendants[lc];
 726                         nodes[i] = nodes[lc];
 727                         for (it = descendants[rc].begin(); it != descendants[rc].end(); it++) {
 728                                 names.insert(*it);
 729                         }
 730                         for (set<int>::iterator itNum = nodes[rc].begin(); itNum != nodes[rc].end(); itNum++) {
 731                                 nodes[i].insert(*itNum);
 732                         }
 733                         //you are your own descendant
 734                         nodes[i].insert(i);
 735                 }
 736
 737                 return names;
 738         }
 739         catch(exception& e) {
 740                 m->errorOut(e, "IndicatorCommand", "getDescendantList");
 741                 exit(1);
 742         }
 743 }
 744 //**********************************************************************************************************************
 745 int IndicatorCommand::getShared(){
 746         try {
 747                 InputData* input = new InputData(sharedfile, "sharedfile");
 748                 lookup = input->getSharedRAbundVectors();
 749                 string lastLabel = lookup[0]->getLabel();
 750
 751                 if (label == "") { label = lastLabel; delete input; return 0; }
 752
 753                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 754                 set<string> labels; labels.insert(label);
 755                 set<string> processedLabels;
 756                 set<string> userLabels = labels;
 757
 758                 //as long as you are not at the end of the file or done wih the lines you want
 759                 while((lookup[0] != NULL) && (userLabels.size() != 0)) {
 760                         if (m->control_pressed) {  delete input; return 0;  }
 761
 762                         if(labels.count(lookup[0]->getLabel()) == 1){
 763                                 processedLabels.insert(lookup[0]->getLabel());
 764                                 userLabels.erase(lookup[0]->getLabel());
 765                                 break;
 766                         }
 767
 768                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 769                                 string saveLabel = lookup[0]->getLabel();
 770
 771                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 772                                 lookup = input->getSharedRAbundVectors(lastLabel);
 773
 774                                 processedLabels.insert(lookup[0]->getLabel());
 775                                 userLabels.erase(lookup[0]->getLabel());
 776
 777                                 //restore real lastlabel to save below
 778                                 lookup[0]->setLabel(saveLabel);
 779                                 break;
 780                         }
 781
 782                         lastLabel = lookup[0]->getLabel();
 783
 784                         //get next line to process
 785                         //prevent memory leak
 786                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 787                         lookup = input->getSharedRAbundVectors();
 788                 }
 789
 790
 791                 if (m->control_pressed) { delete input; return 0;  }
 792
 793                 //output error messages about any remaining user labels
 794                 set<string>::iterator it;
 795                 bool needToRun = false;
 796                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 797                         m->mothurOut("Your file does not include the label " + *it);
 798                         if (processedLabels.count(lastLabel) != 1) {
 799                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 800                                 needToRun = true;
 801                         }else {
 802                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 803                         }
 804                 }
 805
 806                 //run last label if you need to
 807                 if (needToRun == true)  {
 808                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i];       } }
 809                         lookup = input->getSharedRAbundVectors(lastLabel);
 810                 }
 811
 812                 delete input;
 813                 return 0;
 814         }
 815         catch(exception& e) {
 816                 m->errorOut(e, "IndicatorCommand", "getShared");
 817                 exit(1);
 818         }
 819 }
 820 //**********************************************************************************************************************
 821 int IndicatorCommand::getSharedFloat(){
 822         try {
 823                 InputData* input = new InputData(relabundfile, "relabund");
 824                 lookupFloat = input->getSharedRAbundFloatVectors();
 825                 string lastLabel = lookupFloat[0]->getLabel();
 826
 827                 if (label == "") { label = lastLabel; delete input; return 0; }
 828
 829                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 830                 set<string> labels; labels.insert(label);
 831                 set<string> processedLabels;
 832                 set<string> userLabels = labels;
 833
 834                 //as long as you are not at the end of the file or done wih the lines you want
 835                 while((lookupFloat[0] != NULL) && (userLabels.size() != 0)) {
 836
 837                         if (m->control_pressed) {  delete input; return 0;  }
 838
 839                         if(labels.count(lookupFloat[0]->getLabel()) == 1){
 840                                 processedLabels.insert(lookupFloat[0]->getLabel());
 841                                 userLabels.erase(lookupFloat[0]->getLabel());
 842                                 break;
 843                         }
 844
 845                         if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 846                                 string saveLabel = lookupFloat[0]->getLabel();
 847
 848                                 for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 849                                 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 850
 851                                 processedLabels.insert(lookupFloat[0]->getLabel());
 852                                 userLabels.erase(lookupFloat[0]->getLabel());
 853
 854                                 //restore real lastlabel to save below
 855                                 lookupFloat[0]->setLabel(saveLabel);
 856                                 break;
 857                         }
 858
 859                         lastLabel = lookupFloat[0]->getLabel();
 860
 861                         //get next line to process
 862                         //prevent memory leak
 863                         for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 864                         lookupFloat = input->getSharedRAbundFloatVectors();
 865                 }
 866
 867
 868                 if (m->control_pressed) { delete input; return 0;  }
 869
 870                 //output error messages about any remaining user labels
 871                 set<string>::iterator it;
 872                 bool needToRun = false;
 873                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 874                         m->mothurOut("Your file does not include the label " + *it);
 875                         if (processedLabels.count(lastLabel) != 1) {
 876                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 877                                 needToRun = true;
 878                         }else {
 879                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 880                         }
 881                 }
 882
 883                 //run last label if you need to
 884                 if (needToRun == true)  {
 885                         for (int i = 0; i < lookupFloat.size(); i++) {  if (lookupFloat[i] != NULL) {   delete lookupFloat[i];  } }
 886                         lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 887                 }
 888
 889                 delete input;
 890                 return 0;
 891         }
 892         catch(exception& e) {
 893                 m->errorOut(e, "IndicatorCommand", "getShared");
 894         exit(1);
 895         }
 896 }
 897 /*****************************************************************/
 898
 899