treegroupscommand.cpp

   1 /*
   2  *  treegroupscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 4/8/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "treegroupscommand.h"
  11 #include "subsample.h"
  12 #include "consensus.h"
  13
  14 //**********************************************************************************************************************
  15 vector<string> TreeGroupCommand::setParameters(){
  16         try {
  17                 CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);
  18                 CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
  19                 CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName",false,false); parameters.push_back(pname);
  20                 CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "countcolumn",false,false); parameters.push_back(pcount);
  21         CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName-countcolumn",false,false); parameters.push_back(pcolumn);
  22         CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
  23         CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
  24         CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
  25                 CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
  26                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  27                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  28                 CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
  29
  30         CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  31 //CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
  32                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  33                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  34
  35                 vector<string> myArray;
  36                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  37                 return myArray;
  38         }
  39         catch(exception& e) {
  40                 m->errorOut(e, "TreeGroupCommand", "setParameters");
  41                 exit(1);
  42         }
  43 }
  44 //**********************************************************************************************************************
  45 string TreeGroupCommand::getHelpString(){
  46         try {
  47                 string helpString = "";
  48                 ValidCalculators validCalculator;
  49                 helpString += "The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n";
  50                 helpString += "The tree.shared command parameters are shared, groups, calc, phylip, column, name, cutoff, precision, processors, subsample, iters and label.\n";
  51                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
  52                 helpString += "The group names are separated by dashes. The label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n";
  53                 helpString += "The phylip or column parameter are required if you do not provide a sharedfile, and only one may be used.  If you use a column file the name filename is required. \n";
  54                 helpString += "If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n";
  55                 helpString += "The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
  56         helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
  57         helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group. The subsample parameter may only be used with a shared file.\n";
  58                 helpString += "Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n";
  59                 helpString += "The default value for groups is all the groups in your groupfile.\n";
  60                 helpString += "The default value for calc is jclass-thetayc.\n";
  61                 helpString += "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n";
  62                 helpString += validCalculator.printCalc("treegroup");
  63                 helpString += "Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n";
  64                 helpString += "Example tree.shared(phylip=abrecovery.dist).\n";
  65                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  66                 return helpString;
  67         }
  68         catch(exception& e) {
  69                 m->errorOut(e, "TreeGroupCommand", "getHelpString");
  70                 exit(1);
  71         }
  72 }
  73 //**********************************************************************************************************************
  74 string TreeGroupCommand::getOutputFileNameTag(string type, string inputName=""){
  75         try {
  76         string outputFileName = "";
  77                 map<string, vector<string> >::iterator it;
  78
  79         //is this a type this command creates
  80         it = outputTypes.find(type);
  81         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  82         else {
  83             if (type == "tree")            {   outputFileName =  "tre";   }
  84             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  85         }
  86         return outputFileName;
  87         }
  88         catch(exception& e) {
  89                 m->errorOut(e, "TreeGroupCommand", "getOutputFileNameTag");
  90                 exit(1);
  91         }
  92 }
  93 //**********************************************************************************************************************
  94 TreeGroupCommand::TreeGroupCommand(){
  95         try {
  96                 abort = true; calledHelp = true;
  97                 setParameters();
  98                 //initialize outputTypes
  99                 vector<string> tempOutNames;
 100                 outputTypes["tree"] = tempOutNames;
 101         }
 102         catch(exception& e) {
 103                 m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
 104                 exit(1);
 105         }
 106 }
 107 //**********************************************************************************************************************
 108
 109 TreeGroupCommand::TreeGroupCommand(string option)  {
 110         try {
 111                 abort = false; calledHelp = false;
 112                 allLines = 1;
 113
 114                 //allow user to run help
 115                 if(option == "help") { help(); abort = true; calledHelp = true; }
 116                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 117
 118                 else {
 119                         vector<string> myArray = setParameters();
 120
 121                         OptionParser parser(option);
 122                         map<string, string> parameters = parser. getParameters();
 123
 124                         ValidParameters validParameter;
 125                         map<string, string>::iterator it;
 126
 127                         //check to make sure all parameters are valid for command
 128                         for (it = parameters.begin(); it != parameters.end(); it++) {
 129                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 130                         }
 131
 132                         //initialize outputTypes
 133                         vector<string> tempOutNames;
 134                         outputTypes["tree"] = tempOutNames;
 135
 136                         //if the user changes the input directory command factory will send this info to us in the output parameter
 137                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 138                         if (inputDir == "not found"){   inputDir = "";          }
 139                         else {
 140                                 string path;
 141                                 it = parameters.find("phylip");
 142                                 //user has given a template file
 143                                 if(it != parameters.end()){
 144                                         path = m->hasPath(it->second);
 145                                         //if the user has not given a path then, add inputdir. else leave path alone.
 146                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 147                                 }
 148
 149                                 it = parameters.find("column");
 150                                 //user has given a template file
 151                                 if(it != parameters.end()){
 152                                         path = m->hasPath(it->second);
 153                                         //if the user has not given a path then, add inputdir. else leave path alone.
 154                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
 155                                 }
 156
 157                                 it = parameters.find("name");
 158                                 //user has given a template file
 159                                 if(it != parameters.end()){
 160                                         path = m->hasPath(it->second);
 161                                         //if the user has not given a path then, add inputdir. else leave path alone.
 162                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 163                                 }
 164
 165                 it = parameters.find("count");
 166                                 //user has given a template file
 167                                 if(it != parameters.end()){
 168                                         path = m->hasPath(it->second);
 169                                         //if the user has not given a path then, add inputdir. else leave path alone.
 170                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 171                                 }
 172                         }
 173
 174                         //check for required parameters
 175                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 176                         if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 177                         else if (phylipfile == "not found") { phylipfile = ""; }
 178                         else {  inputfile = phylipfile;  format = "phylip"; m->setPhylipFile(phylipfile);       }
 179
 180                         columnfile = validParameter.validFile(parameters, "column", true);
 181                         if (columnfile == "not open") { columnfile = ""; abort = true; }
 182                         else if (columnfile == "not found") { columnfile = ""; }
 183                         else {  inputfile = columnfile; format = "column";      m->setColumnFile(columnfile); }
 184
 185                         sharedfile = validParameter.validFile(parameters, "shared", true);
 186                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 187                         else if (sharedfile == "not found") { sharedfile = ""; }
 188                         else {  inputfile = sharedfile; format = "sharedfile";  m->setSharedFile(sharedfile); }
 189
 190                         namefile = validParameter.validFile(parameters, "name", true);
 191                         if (namefile == "not open") { abort = true; }
 192                         else if (namefile == "not found") { namefile = ""; }
 193                         else { m->setNameFile(namefile); }
 194
 195             countfile = validParameter.validFile(parameters, "count", true);
 196                         if (countfile == "not open") { abort = true; countfile = ""; }
 197                         else if (countfile == "not found") { countfile = ""; }
 198                         else { m->setCountTableFile(countfile); }
 199
 200                         if ((phylipfile == "") && (columnfile == "") && (sharedfile == "")) {
 201                                 //is there are current file available for either of these?
 202                                 //give priority to shared, then column, then phylip
 203                                 sharedfile = m->getSharedFile();
 204                                 if (sharedfile != "") {  inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 205                                 else {
 206                                         columnfile = m->getColumnFile();
 207                                         if (columnfile != "") { inputfile = columnfile; format = "column";  m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
 208                                         else {
 209                                                 phylipfile = m->getPhylipFile();
 210                                                 if (phylipfile != "") { inputfile = phylipfile;  format = "phylip";  m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 211                                                 else {
 212                                                         m->mothurOut("No valid current files. You must provide a shared, phylip or column file."); m->mothurOutEndLine();
 213                                                         abort = true;
 214                                                 }
 215                                         }
 216                                 }
 217                         }
 218                         else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When running the tree.shared command with a distance file you may not use both the column and the phylip parameters."); m->mothurOutEndLine(); abort = true; }
 219
 220                         if (columnfile != "") {
 221                                 if ((namefile == "") && (countfile == "")){
 222                                         namefile = m->getNameFile();
 223                                         if (namefile != "") {  m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
 224                                         else {
 225                                                 countfile = m->getCountTableFile();
 226                         if (countfile != "") {  m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
 227                         else {
 228                             m->mothurOut("You need to provide a namefile or countfile if you are going to use the column format."); m->mothurOutEndLine();
 229                             abort = true;
 230                         }
 231                                         }
 232                                 }
 233                         }
 234
 235
 236                         //check for optional parameter and set defaults
 237                         // ...at some point should added some additional type checking...
 238                         label = validParameter.validFile(parameters, "label", false);
 239                         if (label == "not found") { label = ""; }
 240                         else {
 241                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 242                                 else { allLines = 1;  }
 243                         }
 244
 245                         groups = validParameter.validFile(parameters, "groups", false);
 246                         if (groups == "not found") { groups = ""; }
 247                         else {
 248                                 m->splitAtDash(groups, Groups);
 249                                 m->setGroups(Groups);
 250                         }
 251
 252                         calc = validParameter.validFile(parameters, "calc", false);
 253                         if (calc == "not found") { calc = "jclass-thetayc";  }
 254                         else {
 255                                  if (calc == "default")  {  calc = "jclass-thetayc";  }
 256                         }
 257                         m->splitAtDash(calc, Estimators);
 258                         if (m->inUsersGroups("citation", Estimators)) {
 259                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 260                                 //remove citation from list of calcs
 261                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 262                         }
 263
 264                         string temp;
 265                         temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }
 266                         m->mothurConvert(temp, precision);
 267
 268                         temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10"; }
 269                         m->mothurConvert(temp, cutoff);
 270                         cutoff += (5 / (precision * 10.0));
 271
 272             temp = validParameter.validFile(parameters, "processors", false);   if (temp == "not found"){       temp = m->getProcessors();      }
 273                         m->setProcessors(temp);
 274                         m->mothurConvert(temp, processors);
 275
 276             temp = validParameter.validFile(parameters, "iters", false);                        if (temp == "not found") { temp = "1000"; }
 277                         m->mothurConvert(temp, iters);
 278
 279             temp = validParameter.validFile(parameters, "subsample", false);            if (temp == "not found") { temp = "F"; }
 280                         if (m->isNumeric1(temp)) { m->mothurConvert(temp, subsampleSize); subsample = true; }
 281             else {
 282                 if (m->isTrue(temp)) { subsample = true; subsampleSize = -1; }  //we will set it to smallest group later
 283                 else { subsample = false; }
 284             }
 285
 286             if (subsample == false) { iters = 1; }
 287
 288             if (subsample && (format != "sharedfile")) { m->mothurOut("[ERROR]: the subsample parameter can only be used with a shared file.\n"); abort=true; }
 289
 290                         //if the user changes the output directory command factory will send this info to us in the output parameter
 291                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 292                                 outputDir = "";
 293                                 outputDir += m->hasPath(inputfile); //if user entered a file with a path then preserve it
 294                         }
 295                 }
 296
 297         }
 298         catch(exception& e) {
 299                 m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
 300                 exit(1);
 301         }
 302 }
 303 //**********************************************************************************************************************
 304
 305 TreeGroupCommand::~TreeGroupCommand(){
 306         if (abort == false) {
 307                 if (format == "sharedfile") {  delete input; }
 308                 else { delete list; }
 309                 delete ct;
 310         }
 311
 312 }
 313
 314 //**********************************************************************************************************************
 315
 316 int TreeGroupCommand::execute(){
 317         try {
 318
 319                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 320
 321                 if (format == "sharedfile") {
 322
 323                         ValidCalculators validCalculator;
 324
 325                         for (int i=0; i<Estimators.size(); i++) {
 326                                 if (validCalculator.isValidCalculator("treegroup", Estimators[i]) == true) {
 327                                         if (Estimators[i] == "sharedsobs") {
 328                                                 treeCalculators.push_back(new SharedSobsCS());
 329                                         }else if (Estimators[i] == "sharedchao") {
 330                                                 treeCalculators.push_back(new SharedChao1());
 331                                         }else if (Estimators[i] == "sharedace") {
 332                                                 treeCalculators.push_back(new SharedAce());
 333                                         }else if (Estimators[i] == "jabund") {
 334                                                 treeCalculators.push_back(new JAbund());
 335                                         }else if (Estimators[i] == "sorabund") {
 336                                                 treeCalculators.push_back(new SorAbund());
 337                                         }else if (Estimators[i] == "jclass") {
 338                                                 treeCalculators.push_back(new Jclass());
 339                                         }else if (Estimators[i] == "sorclass") {
 340                                                 treeCalculators.push_back(new SorClass());
 341                                         }else if (Estimators[i] == "jest") {
 342                                                 treeCalculators.push_back(new Jest());
 343                                         }else if (Estimators[i] == "sorest") {
 344                                                 treeCalculators.push_back(new SorEst());
 345                                         }else if (Estimators[i] == "thetayc") {
 346                                                 treeCalculators.push_back(new ThetaYC());
 347                                         }else if (Estimators[i] == "thetan") {
 348                                                 treeCalculators.push_back(new ThetaN());
 349                                         }else if (Estimators[i] == "kstest") {
 350                                                 treeCalculators.push_back(new KSTest());
 351                                         }else if (Estimators[i] == "sharednseqs") {
 352                                                 treeCalculators.push_back(new SharedNSeqs());
 353                                         }else if (Estimators[i] == "ochiai") {
 354                                                 treeCalculators.push_back(new Ochiai());
 355                                         }else if (Estimators[i] == "anderberg") {
 356                                                 treeCalculators.push_back(new Anderberg());
 357                                         }else if (Estimators[i] == "kulczynski") {
 358                                                 treeCalculators.push_back(new Kulczynski());
 359                                         }else if (Estimators[i] == "kulczynskicody") {
 360                                                 treeCalculators.push_back(new KulczynskiCody());
 361                                         }else if (Estimators[i] == "lennon") {
 362                                                 treeCalculators.push_back(new Lennon());
 363                                         }else if (Estimators[i] == "morisitahorn") {
 364                                                 treeCalculators.push_back(new MorHorn());
 365                                         }else if (Estimators[i] == "braycurtis") {
 366                                                 treeCalculators.push_back(new BrayCurtis());
 367                                         }else if (Estimators[i] == "whittaker") {
 368                                                 treeCalculators.push_back(new Whittaker());
 369                                         }else if (Estimators[i] == "odum") {
 370                                                 treeCalculators.push_back(new Odum());
 371                                         }else if (Estimators[i] == "canberra") {
 372                                                 treeCalculators.push_back(new Canberra());
 373                                         }else if (Estimators[i] == "structeuclidean") {
 374                                                 treeCalculators.push_back(new StructEuclidean());
 375                                         }else if (Estimators[i] == "structchord") {
 376                                                 treeCalculators.push_back(new StructChord());
 377                                         }else if (Estimators[i] == "hellinger") {
 378                                                 treeCalculators.push_back(new Hellinger());
 379                                         }else if (Estimators[i] == "manhattan") {
 380                                                 treeCalculators.push_back(new Manhattan());
 381                                         }else if (Estimators[i] == "structpearson") {
 382                                                 treeCalculators.push_back(new StructPearson());
 383                                         }else if (Estimators[i] == "soergel") {
 384                                                 treeCalculators.push_back(new Soergel());
 385                                         }else if (Estimators[i] == "spearman") {
 386                                                 treeCalculators.push_back(new Spearman());
 387                                         }else if (Estimators[i] == "structkulczynski") {
 388                                                 treeCalculators.push_back(new StructKulczynski());
 389                                         }else if (Estimators[i] == "speciesprofile") {
 390                                                 treeCalculators.push_back(new SpeciesProfile());
 391                                         }else if (Estimators[i] == "hamming") {
 392                                                 treeCalculators.push_back(new Hamming());
 393                                         }else if (Estimators[i] == "structchi2") {
 394                                                 treeCalculators.push_back(new StructChi2());
 395                                         }else if (Estimators[i] == "gower") {
 396                                                 treeCalculators.push_back(new Gower());
 397                                         }else if (Estimators[i] == "memchi2") {
 398                                                 treeCalculators.push_back(new MemChi2());
 399                                         }else if (Estimators[i] == "memchord") {
 400                                                 treeCalculators.push_back(new MemChord());
 401                                         }else if (Estimators[i] == "memeuclidean") {
 402                                                 treeCalculators.push_back(new MemEuclidean());
 403                                         }else if (Estimators[i] == "mempearson") {
 404                                                 treeCalculators.push_back(new MemPearson());
 405                                         }
 406                                 }
 407                         }
 408
 409                         //if the users entered no valid calculators don't execute command
 410                         if (treeCalculators.size() == 0) { m->mothurOut("You have given no valid calculators."); m->mothurOutEndLine(); return 0; }
 411
 412                         input = new InputData(sharedfile, "sharedfile");
 413                         lookup = input->getSharedRAbundVectors();
 414                         lastLabel = lookup[0]->getLabel();
 415
 416                         if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); return 0; }
 417
 418                         //used in tree constructor
 419                         m->runParse = false;
 420
 421                         //create treemap class from groupmap for tree class to use
 422                         ct = new CountTable();
 423             set<string> nameMap;
 424             map<string, string> groupMap;
 425             set<string> gps;
 426             for (int i = 0; i < m->getAllGroups().size(); i++) {
 427                 nameMap.insert(m->getAllGroups()[i]);
 428                 gps.insert(m->getAllGroups()[i]);
 429                 groupMap[m->getAllGroups()[i]] = m->getAllGroups()[i];
 430             }
 431             ct->createTable(nameMap, groupMap, gps);
 432
 433                         //clear globaldatas old tree names if any
 434                         m->Treenames.clear();
 435
 436                         //fills globaldatas tree names
 437                         m->Treenames = m->getGroups();
 438
 439                         if (m->control_pressed) { return 0; }
 440
 441                         //create tree file
 442                         makeSimsShared();
 443
 444                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
 445                 }else{
 446                         //read in dist file
 447                         filename = inputfile;
 448
 449             ReadMatrix* readMatrix;
 450                         if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
 451                         else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
 452
 453                         readMatrix->setCutoff(cutoff);
 454
 455             ct = NULL;
 456             nameMap = NULL;
 457             if(namefile != ""){
 458                 nameMap = new NameAssignment(namefile);
 459                 nameMap->readMap();
 460                 readMatrix->read(nameMap);
 461             }else if (countfile != "") {
 462                 ct = new CountTable();
 463                 ct->readTable(countfile);
 464                 readMatrix->read(ct);
 465             }else {
 466                 readMatrix->read(nameMap);
 467             }
 468
 469                         list = readMatrix->getListVector();
 470                         SparseDistanceMatrix* dMatrix = readMatrix->getDMatrix();
 471
 472                         //make treemap
 473             if (ct != NULL) { delete ct; }
 474                         ct = new CountTable();
 475             set<string> nameMap;
 476             map<string, string> groupMap;
 477             set<string> gps;
 478             for (int i = 0; i < list->getNumBins(); i++) {
 479                 string bin = list->get(i);
 480                 nameMap.insert(bin);
 481                 gps.insert(bin);
 482                 groupMap[bin] = bin;
 483             }
 484             ct->createTable(nameMap, groupMap, gps);
 485
 486                         vector<string> namesGroups = ct->getNamesOfGroups();
 487                         m->setGroups(namesGroups);
 488
 489                         //clear globaldatas old tree names if any
 490                         m->Treenames.clear();
 491
 492                         //fills globaldatas tree names
 493                         m->Treenames = m->getGroups();
 494
 495                         //used in tree constructor
 496                         m->runParse = false;
 497
 498                         if (m->control_pressed) { return 0; }
 499
 500                         vector< vector<double> > matrix = makeSimsDist(dMatrix);
 501             delete readMatrix;
 502             delete dMatrix;
 503
 504                         if (m->control_pressed) { return 0; }
 505
 506                         //create a new filename
 507                         string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + getOutputFileNameTag("tree");
 508                         outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 509
 510                         Tree* newTree = createTree(matrix);
 511
 512             if (newTree != NULL) {  writeTree(outputFile, newTree); delete newTree; }
 513
 514                         if (m->control_pressed) { return 0; }
 515
 516                         m->mothurOut("Tree complete. "); m->mothurOutEndLine();
 517
 518                 }
 519
 520                 //reset groups parameter
 521                 m->clearGroups();
 522
 523                 //set tree file as new current treefile
 524                 string current = "";
 525                 itTypes = outputTypes.find("tree");
 526                 if (itTypes != outputTypes.end()) {
 527                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
 528                 }
 529
 530                 m->mothurOutEndLine();
 531                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 532                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 533                 m->mothurOutEndLine();
 534
 535                 return 0;
 536         }
 537         catch(exception& e) {
 538                 m->errorOut(e, "TreeGroupCommand", "execute");
 539                 exit(1);
 540         }
 541 }
 542 //**********************************************************************************************************************
 543
 544 Tree* TreeGroupCommand::createTree(vector< vector<double> >& simMatrix){
 545         try {
 546                 //create tree
 547                 t = new Tree(ct, simMatrix);
 548
 549         if (m->control_pressed) { delete t; t = NULL; return t; }
 550
 551         //assemble tree
 552                 t->assembleTree();
 553
 554                 return t;
 555         }
 556         catch(exception& e) {
 557                 m->errorOut(e, "TreeGroupCommand", "createTree");
 558                 exit(1);
 559         }
 560 }
 561 /***********************************************************/
 562 int TreeGroupCommand::writeTree(string out, Tree* T) {
 563         try {
 564
 565         //print newick file
 566                 t->createNewickFile(out);
 567
 568         if (m->control_pressed) { m->mothurRemove(out); outputNames.pop_back(); return 1; }
 569
 570         return 0;
 571
 572         }
 573         catch(exception& e) {
 574                 m->errorOut(e, "TreeGroupCommand", "printSims");
 575                 exit(1);
 576         }
 577 }
 578
 579 /***********************************************************/
 580 void TreeGroupCommand::printSims(ostream& out, vector< vector<double> >& simMatrix) {
 581         try {
 582
 583         for (int m = 0; m < simMatrix.size(); m++)      {
 584                         //out << lookup[m]->getGroup() << '\t';
 585                         for (int n = 0; n < simMatrix.size(); n++)      {
 586                                 out << simMatrix[m][n] << '\t';
 587                         }
 588                         out << endl;
 589                 }
 590
 591         }
 592         catch(exception& e) {
 593                 m->errorOut(e, "TreeGroupCommand", "printSims");
 594                 exit(1);
 595         }
 596 }
 597 /***********************************************************/
 598 vector< vector<double> > TreeGroupCommand::makeSimsDist(SparseDistanceMatrix* matrix) {
 599         try {
 600                 numGroups = list->size();
 601
 602                 //initialize simMatrix
 603                 vector< vector<double> > simMatrix;
 604                 simMatrix.resize(numGroups);
 605                 for (int k = 0; k < simMatrix.size(); k++)      {
 606                         for (int j = 0; j < simMatrix.size(); j++)      {
 607                                 simMatrix[k].push_back(0.0);
 608                         }
 609                 }
 610
 611                 //go through sparse matrix and fill sims
 612                 //go through each cell in the sparsematrix
 613         for (int i = 0; i < matrix->seqVec.size(); i++) {
 614             for (int j = 0; j < matrix->seqVec[i].size(); j++) {
 615
 616                 //already checked everyone else in row
 617                 if (i < matrix->seqVec[i][j].index) {
 618                     simMatrix[i][matrix->seqVec[i][j].index] = -(matrix->seqVec[i][j].dist -1.0);
 619                     simMatrix[matrix->seqVec[i][j].index][i] = -(matrix->seqVec[i][j].dist -1.0);
 620
 621                     if (m->control_pressed) { return simMatrix; }
 622                 }
 623             }
 624                 }
 625
 626                 return simMatrix;
 627         }
 628         catch(exception& e) {
 629                 m->errorOut(e, "TreeGroupCommand", "makeSimsDist");
 630                 exit(1);
 631         }
 632 }
 633
 634 /***********************************************************/
 635 int TreeGroupCommand::makeSimsShared() {
 636         try {
 637
 638         if (subsample) {
 639             if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
 640                 subsampleSize = lookup[0]->getNumSeqs();
 641                 for (int i = 1; i < lookup.size(); i++) {
 642                     int thisSize = lookup[i]->getNumSeqs();
 643
 644                     if (thisSize < subsampleSize) {     subsampleSize = thisSize;       }
 645                 }
 646             }else {
 647                 m->clearGroups();
 648                 Groups.clear();
 649                 vector<SharedRAbundVector*> temp;
 650                 for (int i = 0; i < lookup.size(); i++) {
 651                     if (lookup[i]->getNumSeqs() < subsampleSize) {
 652                         m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
 653                         delete lookup[i];
 654                     }else {
 655                         Groups.push_back(lookup[i]->getGroup());
 656                         temp.push_back(lookup[i]);
 657                     }
 658                 }
 659                 lookup = temp;
 660                 m->setGroups(Groups);
 661             }
 662
 663             if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
 664         }
 665
 666         numGroups = lookup.size();
 667                 lines.resize(processors);
 668                 for (int i = 0; i < processors; i++) {
 669                         lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
 670                         lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
 671                 }
 672
 673                 set<string> processedLabels;
 674                 set<string> userLabels = labels;
 675
 676                 //as long as you are not at the end of the file or done wih the lines you want
 677                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 678                         if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; } return 1; }
 679
 680                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 681                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 682                                 process(lookup);
 683
 684                                 processedLabels.insert(lookup[0]->getLabel());
 685                                 userLabels.erase(lookup[0]->getLabel());
 686                         }
 687
 688                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 689                                 string saveLabel = lookup[0]->getLabel();
 690
 691                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 692                                 lookup = input->getSharedRAbundVectors(lastLabel);
 693
 694                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 695                                 process(lookup);
 696
 697                                 processedLabels.insert(lookup[0]->getLabel());
 698                                 userLabels.erase(lookup[0]->getLabel());
 699
 700                                 //restore real lastlabel to save below
 701                                 lookup[0]->setLabel(saveLabel);
 702                         }
 703
 704                         lastLabel = lookup[0]->getLabel();
 705
 706                         //get next line to process
 707                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 708                         lookup = input->getSharedRAbundVectors();
 709                 }
 710
 711                 if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; } return 1; }
 712
 713                 //output error messages about any remaining user labels
 714                 set<string>::iterator it;
 715                 bool needToRun = false;
 716                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 717                         m->mothurOut("Your file does not include the label " + *it);
 718                         if (processedLabels.count(lastLabel) != 1) {
 719                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 720                                 needToRun = true;
 721                         }else {
 722                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 723                         }
 724                 }
 725
 726                 //run last label if you need to
 727                 if (needToRun == true)  {
 728                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {             delete lookup[i]; }             }
 729                         lookup = input->getSharedRAbundVectors(lastLabel);
 730
 731                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 732                         process(lookup);
 733                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 734                 }
 735
 736                 for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; }
 737
 738                 return 0;
 739         }
 740         catch(exception& e) {
 741                 m->errorOut(e, "TreeGroupCommand", "makeSimsShared");
 742                 exit(1);
 743         }
 744 }
 745
 746 /***********************************************************/
 747 int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
 748         try{
 749                 vector< vector< vector<seqDist> > > calcDistsTotals;  //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files
 750         vector< vector<seqDist>  > calcDists; calcDists.resize(treeCalculators.size());
 751
 752         for (int thisIter = 0; thisIter < iters; thisIter++) {
 753
 754             vector<SharedRAbundVector*> thisItersLookup = thisLookup;
 755
 756             if (subsample) {
 757                 SubSample sample;
 758                 vector<string> tempLabels; //dont need since we arent printing the sampled sharedRabunds
 759
 760                 //make copy of lookup so we don't get access violations
 761                 vector<SharedRAbundVector*> newLookup;
 762                 for (int k = 0; k < thisItersLookup.size(); k++) {
 763                     SharedRAbundVector* temp = new SharedRAbundVector();
 764                     temp->setLabel(thisItersLookup[k]->getLabel());
 765                     temp->setGroup(thisItersLookup[k]->getGroup());
 766                     newLookup.push_back(temp);
 767                 }
 768
 769                 //for each bin
 770                 for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
 771                     if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
 772                     for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
 773                 }
 774
 775                 tempLabels = sample.getSample(newLookup, subsampleSize);
 776                 thisItersLookup = newLookup;
 777             }
 778
 779             if(processors == 1){
 780                 driver(thisItersLookup, 0, numGroups, calcDists);
 781             }else{
 782                 int process = 1;
 783                 vector<int> processIDS;
 784
 785 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 786                 //loop through and create all the processes you want
 787                 while (process != processors) {
 788                     int pid = fork();
 789
 790                     if (pid > 0) {
 791                         processIDS.push_back(pid);
 792                         process++;
 793                     }else if (pid == 0){
 794
 795                         driver(thisItersLookup, lines[process].start, lines[process].end, calcDists);
 796
 797                         string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(getpid()) + ".dist";
 798                         ofstream outtemp;
 799                         m->openOutputFile(tempdistFileName, outtemp);
 800
 801                         for (int i = 0; i < calcDists.size(); i++) {
 802                             outtemp << calcDists[i].size() << endl;
 803
 804                             for (int j = 0; j < calcDists[i].size(); j++) {
 805                                 outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl;
 806                             }
 807                         }
 808                         outtemp.close();
 809
 810                         exit(0);
 811                     }else {
 812                         m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 813                         for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 814                         exit(0);
 815                     }
 816                 }
 817
 818                 //parent do your part
 819                 driver(thisItersLookup, lines[0].start, lines[0].end, calcDists);
 820
 821                 //force parent to wait until all the processes are done
 822                 for (int i = 0; i < processIDS.size(); i++) {
 823                     int temp = processIDS[i];
 824                     wait(&temp);
 825                 }
 826
 827                 for (int i = 0; i < processIDS.size(); i++) {
 828                     string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(processIDS[i]) +  ".dist";
 829                     ifstream intemp;
 830                     m->openInputFile(tempdistFileName, intemp);
 831
 832                     for (int k = 0; k < calcDists.size(); k++) {
 833                         int size = 0;
 834                         intemp >> size; m->gobble(intemp);
 835
 836                         for (int j = 0; j < size; j++) {
 837                             int seq1 = 0;
 838                             int seq2 = 0;
 839                             float dist = 1.0;
 840
 841                             intemp >> seq1 >> seq2 >> dist;   m->gobble(intemp);
 842
 843                             seqDist tempDist(seq1, seq2, dist);
 844                             calcDists[k].push_back(tempDist);
 845                         }
 846                     }
 847                     intemp.close();
 848                     m->mothurRemove(tempdistFileName);
 849                 }
 850 #else
 851                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 852                 //Windows version shared memory, so be careful when passing variables through the treeSharedData struct.
 853                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 854                 //Taking advantage of shared memory to pass results vectors.
 855                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 856
 857                 vector<treeSharedData*> pDataArray;
 858                 DWORD   dwThreadIdArray[processors-1];
 859                 HANDLE  hThreadArray[processors-1];
 860
 861                 //Create processor worker threads.
 862                 for( int i=1; i<processors; i++ ){
 863
 864                     //make copy of lookup so we don't get access violations
 865                     vector<SharedRAbundVector*> newLookup;
 866                     for (int k = 0; k < thisItersLookup.size(); k++) {
 867                         SharedRAbundVector* temp = new SharedRAbundVector();
 868                         temp->setLabel(thisItersLookup[k]->getLabel());
 869                         temp->setGroup(thisItersLookup[k]->getGroup());
 870                         newLookup.push_back(temp);
 871                     }
 872
 873                     //for each bin
 874                     for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
 875                         if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
 876                         for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
 877                     }
 878
 879                     // Allocate memory for thread data.
 880                     treeSharedData* tempSum = new treeSharedData(m, lines[i].start, lines[i].end, Estimators, newLookup);
 881                     pDataArray.push_back(tempSum);
 882                     processIDS.push_back(i);
 883
 884                     hThreadArray[i-1] = CreateThread(NULL, 0, MyTreeSharedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
 885                 }
 886
 887                 //parent do your part
 888                 driver(thisItersLookup, lines[0].start, lines[0].end, calcDists);
 889
 890                 //Wait until all threads have terminated.
 891                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 892
 893                 //Close all thread handles and free memory allocations.
 894                 for(int i=0; i < pDataArray.size(); i++){
 895                     for (int j = 0; j < pDataArray[i]->thisLookup.size(); j++) {  delete pDataArray[i]->thisLookup[j];  }
 896
 897                     for (int k = 0; k < calcDists.size(); k++) {
 898                         int size = pDataArray[i]->calcDists[k].size();
 899                         for (int j = 0; j < size; j++) {    calcDists[k].push_back(pDataArray[i]->calcDists[k][j]);    }
 900                     }
 901
 902                     CloseHandle(hThreadArray[i]);
 903                     delete pDataArray[i];
 904                 }
 905
 906 #endif
 907             }
 908
 909             calcDistsTotals.push_back(calcDists);
 910
 911             if (subsample) {
 912
 913                 //clean up memory
 914                 for (int i = 0; i < thisItersLookup.size(); i++) { delete thisItersLookup[i]; }
 915                 thisItersLookup.clear();
 916                 for (int i = 0; i < calcDists.size(); i++) {  calcDists[i].clear(); }
 917             }
 918                 }
 919
 920         if (iters != 1) {
 921             //we need to find the average distance and standard deviation for each groups distance
 922
 923             vector< vector<seqDist>  > calcAverages; calcAverages.resize(treeCalculators.size());
 924             for (int i = 0; i < calcAverages.size(); i++) {  //initialize sums to zero.
 925                 calcAverages[i].resize(calcDistsTotals[0][i].size());
 926
 927                 for (int j = 0; j < calcAverages[i].size(); j++) {
 928                     calcAverages[i][j].seq1 = calcDists[i][j].seq1;
 929                     calcAverages[i][j].seq2 = calcDists[i][j].seq2;
 930                     calcAverages[i][j].dist = 0.0;
 931                 }
 932             }
 933
 934             for (int thisIter = 0; thisIter < iters; thisIter++) { //sum all groups dists for each calculator
 935                 for (int i = 0; i < calcAverages.size(); i++) {  //initialize sums to zero.
 936                     for (int j = 0; j < calcAverages[i].size(); j++) {
 937                         calcAverages[i][j].dist += calcDistsTotals[thisIter][i][j].dist;
 938                     }
 939                 }
 940             }
 941
 942             for (int i = 0; i < calcAverages.size(); i++) {  //finds average.
 943                 for (int j = 0; j < calcAverages[i].size(); j++) {
 944                     calcAverages[i][j].dist /= (float) iters;
 945                 }
 946             }
 947
 948             //create average tree for each calc
 949             for (int i = 0; i < calcDists.size(); i++) {
 950                 vector< vector<double> > matrix; //square matrix to represent the distance
 951                 matrix.resize(thisLookup.size());
 952                 for (int k = 0; k < thisLookup.size(); k++) {  matrix[k].resize(thisLookup.size(), 0.0); }
 953
 954                 for (int j = 0; j < calcAverages[i].size(); j++) {
 955                     int row = calcAverages[i][j].seq1;
 956                     int column = calcAverages[i][j].seq2;
 957                     float dist = calcAverages[i][j].dist;
 958
 959                     matrix[row][column] = dist;
 960                     matrix[column][row] = dist;
 961                 }
 962
 963                 //create a new filename
 964                 string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".ave." + getOutputFileNameTag("tree");
 965                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 966
 967                 //creates tree from similarity matrix and write out file
 968                 Tree* newTree = createTree(matrix);
 969                 if (newTree != NULL) { writeTree(outputFile, newTree); }
 970             }
 971
 972             //create all trees for each calc and find their consensus tree
 973             for (int i = 0; i < calcDists.size(); i++) {
 974                 if (m->control_pressed) { break; }
 975
 976                 //create a new filename
 977                 string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".all." + getOutputFileNameTag("tree");
 978                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 979
 980                 ofstream outAll;
 981                 m->openOutputFile(outputFile, outAll);
 982
 983                 vector<Tree*> trees;
 984                 for (int myIter = 0; myIter < iters; myIter++) {
 985
 986                     if(m->control_pressed) { break; }
 987
 988                     //initialize matrix
 989                     vector< vector<double> > matrix; //square matrix to represent the distance
 990                     matrix.resize(thisLookup.size());
 991                     for (int k = 0; k < thisLookup.size(); k++) {  matrix[k].resize(thisLookup.size(), 0.0); }
 992
 993                     for (int j = 0; j < calcDistsTotals[myIter][i].size(); j++) {
 994                         int row = calcDistsTotals[myIter][i][j].seq1;
 995                         int column = calcDistsTotals[myIter][i][j].seq2;
 996                         double dist = calcDistsTotals[myIter][i][j].dist;
 997
 998                         matrix[row][column] = dist;
 999                         matrix[column][row] = dist;
1000                     }
1001
1002                     //creates tree from similarity matrix and write out file
1003                     Tree* newTree = createTree(matrix);
1004                     if (newTree != NULL) {
1005                         newTree->print(outAll);
1006                         trees.push_back(newTree);
1007                     }
1008                 }
1009                 outAll.close();
1010                 if (m->control_pressed) { for (int k = 0; k < trees.size(); k++) { delete trees[k]; } }
1011
1012                 Consensus consensus;
1013                 //clear old tree names if any
1014                 m->Treenames.clear(); m->Treenames = m->getGroups(); //may have changed if subsample eliminated groups
1015                 Tree* conTree = consensus.getTree(trees);
1016
1017                 //create a new filename
1018                 string conFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".cons." + getOutputFileNameTag("tree");
1019                 outputNames.push_back(conFile); outputTypes["tree"].push_back(conFile);
1020                 ofstream outTree;
1021                 m->openOutputFile(conFile, outTree);
1022
1023                 if (conTree != NULL) { conTree->print(outTree, "boot"); delete conTree; }
1024             }
1025
1026         }else {
1027
1028             for (int i = 0; i < calcDists.size(); i++) {
1029                 if (m->control_pressed) { break; }
1030
1031                 //initialize matrix
1032                 vector< vector<double> > matrix; //square matrix to represent the distance
1033                 matrix.resize(thisLookup.size());
1034                 for (int k = 0; k < thisLookup.size(); k++) {  matrix[k].resize(thisLookup.size(), 0.0); }
1035
1036                 for (int j = 0; j < calcDists[i].size(); j++) {
1037                     int row = calcDists[i][j].seq1;
1038                     int column = calcDists[i][j].seq2;
1039                     double dist = calcDists[i][j].dist;
1040
1041                     matrix[row][column] = dist;
1042                     matrix[column][row] = dist;
1043                 }
1044
1045                 //create a new filename
1046                 string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + getOutputFileNameTag("tree");
1047                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
1048
1049                 //creates tree from similarity matrix and write out file
1050                 Tree* newTree = createTree(matrix);
1051                 if (newTree != NULL) { writeTree(outputFile, newTree); delete newTree; }
1052             }
1053         }
1054
1055                 return 0;
1056         }
1057         catch(exception& e) {
1058                 m->errorOut(e, "TreeGroupCommand", "process");
1059                 exit(1);
1060         }
1061 }
1062 /**************************************************************************************************/
1063 int TreeGroupCommand::driver(vector<SharedRAbundVector*> thisLookup, int start, int end, vector< vector<seqDist> >& calcDists) {
1064         try {
1065                 vector<SharedRAbundVector*> subset;
1066                 for (int k = start; k < end; k++) { // pass cdd each set of groups to compare
1067
1068                         for (int l = 0; l < k; l++) {
1069
1070                                 if (k != l) { //we dont need to similiarity of a groups to itself
1071                                         subset.clear(); //clear out old pair of sharedrabunds
1072                                         //add new pair of sharedrabunds
1073                                         subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
1074
1075                                         for(int i=0;i<treeCalculators.size();i++) {
1076
1077                                                 //if this calc needs all groups to calculate the pair load all groups
1078                                                 if (treeCalculators[i]->getNeedsAll()) {
1079                                                         //load subset with rest of lookup for those calcs that need everyone to calc for a pair
1080                                                         for (int w = 0; w < thisLookup.size(); w++) {
1081                                                                 if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
1082                                                         }
1083                                                 }
1084
1085                                                 vector<double> tempdata = treeCalculators[i]->getValues(subset); //saves the calculator outputs
1086
1087                                                 if (m->control_pressed) { return 1; }
1088
1089                                                 seqDist temp(l, k, -(tempdata[0]-1.0));
1090                                                 calcDists[i].push_back(temp);
1091                                         }
1092                                 }
1093                         }
1094                 }
1095
1096                 return 0;
1097         }
1098         catch(exception& e) {
1099                 m->errorOut(e, "TreeGroupCommand", "driver");
1100                 exit(1);
1101         }
1102 }
1103 /***********************************************************/
1104
1105
1106