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","tree",false,false,true); parameters.push_back(pshared);
  18                 CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","tree",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","tree",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-jsd-rjsd", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
  29
  30         CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); 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::getOutputPattern(string type) {
  75     try {
  76         string pattern = "";
  77
  78         if (type == "tree") {  pattern = "[filename],[calc],[distance],[tag],tre-[filename],tre"; }
  79         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  80
  81         return pattern;
  82     }
  83     catch(exception& e) {
  84         m->errorOut(e, "TreeGroupCommand", "getOutputPattern");
  85         exit(1);
  86     }
  87 }
  88 //**********************************************************************************************************************
  89 TreeGroupCommand::TreeGroupCommand(){
  90         try {
  91                 abort = true; calledHelp = true;
  92                 setParameters();
  93                 //initialize outputTypes
  94                 vector<string> tempOutNames;
  95                 outputTypes["tree"] = tempOutNames;
  96         }
  97         catch(exception& e) {
  98                 m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
  99                 exit(1);
 100         }
 101 }
 102 //**********************************************************************************************************************
 103
 104 TreeGroupCommand::TreeGroupCommand(string option)  {
 105         try {
 106                 abort = false; calledHelp = false;
 107                 allLines = 1;
 108
 109                 //allow user to run help
 110                 if(option == "help") { help(); abort = true; calledHelp = true; }
 111                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 112
 113                 else {
 114                         vector<string> myArray = setParameters();
 115
 116                         OptionParser parser(option);
 117                         map<string, string> parameters = parser. getParameters();
 118
 119                         ValidParameters validParameter;
 120                         map<string, string>::iterator it;
 121
 122                         //check to make sure all parameters are valid for command
 123                         for (it = parameters.begin(); it != parameters.end(); it++) {
 124                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 125                         }
 126
 127                         //initialize outputTypes
 128                         vector<string> tempOutNames;
 129                         outputTypes["tree"] = tempOutNames;
 130
 131                         //if the user changes the input directory command factory will send this info to us in the output parameter
 132                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 133                         if (inputDir == "not found"){   inputDir = "";          }
 134                         else {
 135                                 string path;
 136                                 it = parameters.find("phylip");
 137                                 //user has given a template file
 138                                 if(it != parameters.end()){
 139                                         path = m->hasPath(it->second);
 140                                         //if the user has not given a path then, add inputdir. else leave path alone.
 141                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 142                                 }
 143
 144                                 it = parameters.find("column");
 145                                 //user has given a template file
 146                                 if(it != parameters.end()){
 147                                         path = m->hasPath(it->second);
 148                                         //if the user has not given a path then, add inputdir. else leave path alone.
 149                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
 150                                 }
 151
 152                                 it = parameters.find("name");
 153                                 //user has given a template file
 154                                 if(it != parameters.end()){
 155                                         path = m->hasPath(it->second);
 156                                         //if the user has not given a path then, add inputdir. else leave path alone.
 157                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 158                                 }
 159
 160                 it = parameters.find("count");
 161                                 //user has given a template file
 162                                 if(it != parameters.end()){
 163                                         path = m->hasPath(it->second);
 164                                         //if the user has not given a path then, add inputdir. else leave path alone.
 165                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 166                                 }
 167                         }
 168
 169                         //check for required parameters
 170                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 171                         if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 172                         else if (phylipfile == "not found") { phylipfile = ""; }
 173                         else {  inputfile = phylipfile;  format = "phylip"; m->setPhylipFile(phylipfile);       }
 174
 175                         columnfile = validParameter.validFile(parameters, "column", true);
 176                         if (columnfile == "not open") { columnfile = ""; abort = true; }
 177                         else if (columnfile == "not found") { columnfile = ""; }
 178                         else {  inputfile = columnfile; format = "column";      m->setColumnFile(columnfile); }
 179
 180                         sharedfile = validParameter.validFile(parameters, "shared", true);
 181                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 182                         else if (sharedfile == "not found") { sharedfile = ""; }
 183                         else {  inputfile = sharedfile; format = "sharedfile";  m->setSharedFile(sharedfile); }
 184
 185                         namefile = validParameter.validFile(parameters, "name", true);
 186                         if (namefile == "not open") { abort = true; }
 187                         else if (namefile == "not found") { namefile = ""; }
 188                         else { m->setNameFile(namefile); }
 189
 190             countfile = validParameter.validFile(parameters, "count", true);
 191                         if (countfile == "not open") { abort = true; countfile = ""; }
 192                         else if (countfile == "not found") { countfile = ""; }
 193                         else { m->setCountTableFile(countfile); }
 194
 195                         if ((phylipfile == "") && (columnfile == "") && (sharedfile == "")) {
 196                                 //is there are current file available for either of these?
 197                                 //give priority to shared, then column, then phylip
 198                                 sharedfile = m->getSharedFile();
 199                                 if (sharedfile != "") {  inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 200                                 else {
 201                                         columnfile = m->getColumnFile();
 202                                         if (columnfile != "") { inputfile = columnfile; format = "column";  m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
 203                                         else {
 204                                                 phylipfile = m->getPhylipFile();
 205                                                 if (phylipfile != "") { inputfile = phylipfile;  format = "phylip";  m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 206                                                 else {
 207                                                         m->mothurOut("No valid current files. You must provide a shared, phylip or column file."); m->mothurOutEndLine();
 208                                                         abort = true;
 209                                                 }
 210                                         }
 211                                 }
 212                         }
 213                         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; }
 214
 215                         if (columnfile != "") {
 216                                 if ((namefile == "") && (countfile == "")){
 217                                         namefile = m->getNameFile();
 218                                         if (namefile != "") {  m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
 219                                         else {
 220                                                 countfile = m->getCountTableFile();
 221                         if (countfile != "") {  m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
 222                         else {
 223                             m->mothurOut("You need to provide a namefile or countfile if you are going to use the column format."); m->mothurOutEndLine();
 224                             abort = true;
 225                         }
 226                                         }
 227                                 }
 228                         }
 229
 230
 231                         //check for optional parameter and set defaults
 232                         // ...at some point should added some additional type checking...
 233                         label = validParameter.validFile(parameters, "label", false);
 234                         if (label == "not found") { label = ""; }
 235                         else {
 236                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 237                                 else { allLines = 1;  }
 238                         }
 239
 240                         groups = validParameter.validFile(parameters, "groups", false);
 241                         if (groups == "not found") { groups = ""; }
 242                         else {
 243                                 m->splitAtDash(groups, Groups);
 244                                 m->setGroups(Groups);
 245                         }
 246
 247                         calc = validParameter.validFile(parameters, "calc", false);
 248                         if (calc == "not found") { calc = "jclass-thetayc";  }
 249                         else {
 250                                  if (calc == "default")  {  calc = "jclass-thetayc";  }
 251                         }
 252                         m->splitAtDash(calc, Estimators);
 253                         if (m->inUsersGroups("citation", Estimators)) {
 254                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 255                                 //remove citation from list of calcs
 256                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 257                         }
 258
 259                         string temp;
 260                         temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }
 261                         m->mothurConvert(temp, precision);
 262
 263                         temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10"; }
 264                         m->mothurConvert(temp, cutoff);
 265                         cutoff += (5 / (precision * 10.0));
 266
 267             temp = validParameter.validFile(parameters, "processors", false);   if (temp == "not found"){       temp = m->getProcessors();      }
 268                         m->setProcessors(temp);
 269                         m->mothurConvert(temp, processors);
 270
 271             temp = validParameter.validFile(parameters, "iters", false);                        if (temp == "not found") { temp = "1000"; }
 272                         m->mothurConvert(temp, iters);
 273
 274             temp = validParameter.validFile(parameters, "subsample", false);            if (temp == "not found") { temp = "F"; }
 275                         if (m->isNumeric1(temp)) { m->mothurConvert(temp, subsampleSize); subsample = true; }
 276             else {
 277                 if (m->isTrue(temp)) { subsample = true; subsampleSize = -1; }  //we will set it to smallest group later
 278                 else { subsample = false; }
 279             }
 280
 281             if (subsample == false) { iters = 1; }
 282
 283             if (subsample && (format != "sharedfile")) { m->mothurOut("[ERROR]: the subsample parameter can only be used with a shared file.\n"); abort=true; }
 284
 285                         //if the user changes the output directory command factory will send this info to us in the output parameter
 286                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 287                                 outputDir = "";
 288                                 outputDir += m->hasPath(inputfile); //if user entered a file with a path then preserve it
 289                         }
 290                 }
 291
 292         }
 293         catch(exception& e) {
 294                 m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
 295                 exit(1);
 296         }
 297 }
 298 //**********************************************************************************************************************
 299
 300 TreeGroupCommand::~TreeGroupCommand(){
 301         if (abort == false) {
 302                 if (format == "sharedfile") {  delete input; }
 303                 else { delete list; }
 304                 delete ct;
 305         }
 306
 307 }
 308
 309 //**********************************************************************************************************************
 310
 311 int TreeGroupCommand::execute(){
 312         try {
 313
 314                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 315
 316                 if (format == "sharedfile") {
 317
 318                         ValidCalculators validCalculator;
 319
 320                         for (int i=0; i<Estimators.size(); i++) {
 321                                 if (validCalculator.isValidCalculator("treegroup", Estimators[i]) == true) {
 322                                         if (Estimators[i] == "sharedsobs") {
 323                                                 treeCalculators.push_back(new SharedSobsCS());
 324                                         }else if (Estimators[i] == "sharedchao") {
 325                                                 treeCalculators.push_back(new SharedChao1());
 326                                         }else if (Estimators[i] == "sharedace") {
 327                                                 treeCalculators.push_back(new SharedAce());
 328                                         }else if (Estimators[i] == "jabund") {
 329                                                 treeCalculators.push_back(new JAbund());
 330                                         }else if (Estimators[i] == "sorabund") {
 331                                                 treeCalculators.push_back(new SorAbund());
 332                                         }else if (Estimators[i] == "jclass") {
 333                                                 treeCalculators.push_back(new Jclass());
 334                                         }else if (Estimators[i] == "sorclass") {
 335                                                 treeCalculators.push_back(new SorClass());
 336                                         }else if (Estimators[i] == "jest") {
 337                                                 treeCalculators.push_back(new Jest());
 338                                         }else if (Estimators[i] == "sorest") {
 339                                                 treeCalculators.push_back(new SorEst());
 340                                         }else if (Estimators[i] == "thetayc") {
 341                                                 treeCalculators.push_back(new ThetaYC());
 342                                         }else if (Estimators[i] == "thetan") {
 343                                                 treeCalculators.push_back(new ThetaN());
 344                                         }else if (Estimators[i] == "kstest") {
 345                                                 treeCalculators.push_back(new KSTest());
 346                                         }else if (Estimators[i] == "sharednseqs") {
 347                                                 treeCalculators.push_back(new SharedNSeqs());
 348                                         }else if (Estimators[i] == "ochiai") {
 349                                                 treeCalculators.push_back(new Ochiai());
 350                                         }else if (Estimators[i] == "anderberg") {
 351                                                 treeCalculators.push_back(new Anderberg());
 352                                         }else if (Estimators[i] == "kulczynski") {
 353                                                 treeCalculators.push_back(new Kulczynski());
 354                                         }else if (Estimators[i] == "kulczynskicody") {
 355                                                 treeCalculators.push_back(new KulczynskiCody());
 356                                         }else if (Estimators[i] == "lennon") {
 357                                                 treeCalculators.push_back(new Lennon());
 358                                         }else if (Estimators[i] == "morisitahorn") {
 359                                                 treeCalculators.push_back(new MorHorn());
 360                                         }else if (Estimators[i] == "braycurtis") {
 361                                                 treeCalculators.push_back(new BrayCurtis());
 362                                         }else if (Estimators[i] == "whittaker") {
 363                                                 treeCalculators.push_back(new Whittaker());
 364                                         }else if (Estimators[i] == "odum") {
 365                                                 treeCalculators.push_back(new Odum());
 366                                         }else if (Estimators[i] == "canberra") {
 367                                                 treeCalculators.push_back(new Canberra());
 368                                         }else if (Estimators[i] == "structeuclidean") {
 369                                                 treeCalculators.push_back(new StructEuclidean());
 370                                         }else if (Estimators[i] == "structchord") {
 371                                                 treeCalculators.push_back(new StructChord());
 372                                         }else if (Estimators[i] == "hellinger") {
 373                                                 treeCalculators.push_back(new Hellinger());
 374                                         }else if (Estimators[i] == "manhattan") {
 375                                                 treeCalculators.push_back(new Manhattan());
 376                                         }else if (Estimators[i] == "structpearson") {
 377                                                 treeCalculators.push_back(new StructPearson());
 378                                         }else if (Estimators[i] == "soergel") {
 379                                                 treeCalculators.push_back(new Soergel());
 380                                         }else if (Estimators[i] == "spearman") {
 381                                                 treeCalculators.push_back(new Spearman());
 382                                         }else if (Estimators[i] == "structkulczynski") {
 383                                                 treeCalculators.push_back(new StructKulczynski());
 384                                         }else if (Estimators[i] == "speciesprofile") {
 385                                                 treeCalculators.push_back(new SpeciesProfile());
 386                                         }else if (Estimators[i] == "hamming") {
 387                                                 treeCalculators.push_back(new Hamming());
 388                                         }else if (Estimators[i] == "structchi2") {
 389                                                 treeCalculators.push_back(new StructChi2());
 390                                         }else if (Estimators[i] == "gower") {
 391                                                 treeCalculators.push_back(new Gower());
 392                                         }else if (Estimators[i] == "memchi2") {
 393                                                 treeCalculators.push_back(new MemChi2());
 394                                         }else if (Estimators[i] == "memchord") {
 395                                                 treeCalculators.push_back(new MemChord());
 396                                         }else if (Estimators[i] == "memeuclidean") {
 397                                                 treeCalculators.push_back(new MemEuclidean());
 398                                         }else if (Estimators[i] == "mempearson") {
 399                                                 treeCalculators.push_back(new MemPearson());
 400                     }else if (Estimators[i] == "jsd") {
 401                         treeCalculators.push_back(new JSD());
 402                     }else if (Estimators[i] == "rjsd") {
 403                         treeCalculators.push_back(new RJSD());
 404                     }
 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             for (int k = 0; k < lookup.size(); k++) {
 439                 m->Treenames.push_back(lookup[k]->getGroup());
 440             }
 441
 442                         if (m->control_pressed) { return 0; }
 443
 444                         //create tree file
 445                         makeSimsShared();
 446
 447                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
 448                 }else{
 449                         //read in dist file
 450                         filename = inputfile;
 451
 452             ReadMatrix* readMatrix;
 453                         if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
 454                         else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
 455
 456                         readMatrix->setCutoff(cutoff);
 457
 458             ct = NULL;
 459             nameMap = NULL;
 460             if(namefile != ""){
 461                 nameMap = new NameAssignment(namefile);
 462                 nameMap->readMap();
 463                 readMatrix->read(nameMap);
 464             }else if (countfile != "") {
 465                 ct = new CountTable();
 466                 ct->readTable(countfile, true, false);
 467                 readMatrix->read(ct);
 468             }else {
 469                 readMatrix->read(nameMap);
 470             }
 471
 472                         list = readMatrix->getListVector();
 473                         SparseDistanceMatrix* dMatrix = readMatrix->getDMatrix();
 474
 475             //clear globaldatas old tree names if any
 476                         m->Treenames.clear();
 477
 478                         //make treemap
 479             if (ct != NULL) { delete ct; }
 480                         ct = new CountTable();
 481             set<string> nameMap;
 482             map<string, string> groupMap;
 483             set<string> gps;
 484             for (int i = 0; i < list->getNumBins(); i++) {
 485                 string bin = list->get(i);
 486                 nameMap.insert(bin);
 487                 gps.insert(bin);
 488                 groupMap[bin] = bin;
 489                 m->Treenames.push_back(bin);
 490             }
 491             ct->createTable(nameMap, groupMap, gps);
 492
 493                         vector<string> namesGroups = ct->getNamesOfGroups();
 494                         m->setGroups(namesGroups);
 495
 496                         //used in tree constructor
 497                         m->runParse = false;
 498
 499                         if (m->control_pressed) { return 0; }
 500
 501                         vector< vector<double> > matrix = makeSimsDist(dMatrix);
 502             delete readMatrix;
 503             delete dMatrix;
 504
 505                         if (m->control_pressed) { return 0; }
 506
 507                         //create a new filename
 508             map<string, string> variables;
 509             variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
 510                         string outputFile = getOutputFileName("tree",variables);
 511                         outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 512
 513                         Tree* newTree = createTree(matrix);
 514
 515             if (newTree != NULL) {  writeTree(outputFile, newTree); delete newTree; }
 516
 517                         if (m->control_pressed) { return 0; }
 518
 519                         m->mothurOut("Tree complete. "); m->mothurOutEndLine();
 520
 521                 }
 522
 523                 //reset groups parameter
 524                 m->clearGroups();
 525
 526                 //set tree file as new current treefile
 527                 string current = "";
 528                 itTypes = outputTypes.find("tree");
 529                 if (itTypes != outputTypes.end()) {
 530                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
 531                 }
 532
 533                 m->mothurOutEndLine();
 534                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 535                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 536                 m->mothurOutEndLine();
 537
 538                 return 0;
 539         }
 540         catch(exception& e) {
 541                 m->errorOut(e, "TreeGroupCommand", "execute");
 542                 exit(1);
 543         }
 544 }
 545 //**********************************************************************************************************************
 546
 547 Tree* TreeGroupCommand::createTree(vector< vector<double> >& simMatrix){
 548         try {
 549                 //create tree
 550                 t = new Tree(ct, simMatrix);
 551
 552         if (m->control_pressed) { delete t; t = NULL; return t; }
 553
 554         //assemble tree
 555                 t->assembleTree();
 556
 557                 return t;
 558         }
 559         catch(exception& e) {
 560                 m->errorOut(e, "TreeGroupCommand", "createTree");
 561                 exit(1);
 562         }
 563 }
 564 /***********************************************************/
 565 int TreeGroupCommand::writeTree(string out, Tree* T) {
 566         try {
 567
 568         //print newick file
 569                 t->createNewickFile(out);
 570
 571         if (m->control_pressed) { m->mothurRemove(out); outputNames.pop_back(); return 1; }
 572
 573         return 0;
 574
 575         }
 576         catch(exception& e) {
 577                 m->errorOut(e, "TreeGroupCommand", "printSims");
 578                 exit(1);
 579         }
 580 }
 581
 582 /***********************************************************/
 583 void TreeGroupCommand::printSims(ostream& out, vector< vector<double> >& simMatrix) {
 584         try {
 585
 586         for (int m = 0; m < simMatrix.size(); m++)      {
 587                         //out << lookup[m]->getGroup() << '\t';
 588                         for (int n = 0; n < simMatrix.size(); n++)      {
 589                                 out << simMatrix[m][n] << '\t';
 590                         }
 591                         out << endl;
 592                 }
 593
 594         }
 595         catch(exception& e) {
 596                 m->errorOut(e, "TreeGroupCommand", "printSims");
 597                 exit(1);
 598         }
 599 }
 600 /***********************************************************/
 601 vector< vector<double> > TreeGroupCommand::makeSimsDist(SparseDistanceMatrix* matrix) {
 602         try {
 603                 numGroups = list->size();
 604
 605                 //initialize simMatrix
 606                 vector< vector<double> > simMatrix;
 607                 simMatrix.resize(numGroups);
 608                 for (int k = 0; k < simMatrix.size(); k++)      {
 609                         for (int j = 0; j < simMatrix.size(); j++)      {
 610                                 simMatrix[k].push_back(0.0);
 611                         }
 612                 }
 613
 614                 //go through sparse matrix and fill sims
 615                 //go through each cell in the sparsematrix
 616         for (int i = 0; i < matrix->seqVec.size(); i++) {
 617             for (int j = 0; j < matrix->seqVec[i].size(); j++) {
 618
 619                 //already checked everyone else in row
 620                 if (i < matrix->seqVec[i][j].index) {
 621                     simMatrix[i][matrix->seqVec[i][j].index] = -(matrix->seqVec[i][j].dist -1.0);
 622                     simMatrix[matrix->seqVec[i][j].index][i] = -(matrix->seqVec[i][j].dist -1.0);
 623
 624                     if (m->control_pressed) { return simMatrix; }
 625                 }
 626             }
 627                 }
 628
 629                 return simMatrix;
 630         }
 631         catch(exception& e) {
 632                 m->errorOut(e, "TreeGroupCommand", "makeSimsDist");
 633                 exit(1);
 634         }
 635 }
 636
 637 /***********************************************************/
 638 int TreeGroupCommand::makeSimsShared() {
 639         try {
 640
 641         if (subsample) {
 642             if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
 643                 subsampleSize = lookup[0]->getNumSeqs();
 644                 for (int i = 1; i < lookup.size(); i++) {
 645                     int thisSize = lookup[i]->getNumSeqs();
 646
 647                     if (thisSize < subsampleSize) {     subsampleSize = thisSize;       }
 648                 }
 649             }else {
 650                 m->clearGroups();
 651                 Groups.clear();
 652                 m->Treenames.clear();
 653                 vector<SharedRAbundVector*> temp;
 654                 for (int i = 0; i < lookup.size(); i++) {
 655                     if (lookup[i]->getNumSeqs() < subsampleSize) {
 656                         m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
 657                         delete lookup[i];
 658                     }else {
 659                         Groups.push_back(lookup[i]->getGroup());
 660                         temp.push_back(lookup[i]);
 661                         m->Treenames.push_back(lookup[i]->getGroup());
 662                     }
 663                 }
 664                 lookup = temp;
 665                 m->setGroups(Groups);
 666             }
 667
 668             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; }
 669         }
 670         numGroups = lookup.size();
 671
 672         //sanity check to make sure processors < numComparisions
 673         int numDists = 0;
 674         for(int i=0;i<numGroups;i++){
 675             for(int j=0;j<i;j++){
 676                 numDists++;
 677                 if (numDists > processors) { break; }
 678             }
 679         }
 680         if (numDists < processors) { processors = numDists; }
 681
 682                 lines.resize(processors);
 683                 for (int i = 0; i < processors; i++) {
 684                         lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
 685                         lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
 686                 }
 687
 688                 set<string> processedLabels;
 689                 set<string> userLabels = labels;
 690
 691                 //as long as you are not at the end of the file or done wih the lines you want
 692                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 693                         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; }
 694
 695                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 696                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 697                                 process(lookup);
 698
 699                                 processedLabels.insert(lookup[0]->getLabel());
 700                                 userLabels.erase(lookup[0]->getLabel());
 701                         }
 702
 703                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 704                                 string saveLabel = lookup[0]->getLabel();
 705
 706                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 707                                 lookup = input->getSharedRAbundVectors(lastLabel);
 708
 709                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 710                                 process(lookup);
 711
 712                                 processedLabels.insert(lookup[0]->getLabel());
 713                                 userLabels.erase(lookup[0]->getLabel());
 714
 715                                 //restore real lastlabel to save below
 716                                 lookup[0]->setLabel(saveLabel);
 717                         }
 718
 719                         lastLabel = lookup[0]->getLabel();
 720
 721                         //get next line to process
 722                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 723                         lookup = input->getSharedRAbundVectors();
 724                 }
 725
 726                 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; }
 727
 728                 //output error messages about any remaining user labels
 729                 set<string>::iterator it;
 730                 bool needToRun = false;
 731                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 732                         m->mothurOut("Your file does not include the label " + *it);
 733                         if (processedLabels.count(lastLabel) != 1) {
 734                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 735                                 needToRun = true;
 736                         }else {
 737                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 738                         }
 739                 }
 740
 741                 //run last label if you need to
 742                 if (needToRun == true)  {
 743                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {             delete lookup[i]; }             }
 744                         lookup = input->getSharedRAbundVectors(lastLabel);
 745
 746                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 747                         process(lookup);
 748                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 749                 }
 750
 751                 for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; }
 752
 753                 return 0;
 754         }
 755         catch(exception& e) {
 756                 m->errorOut(e, "TreeGroupCommand", "makeSimsShared");
 757                 exit(1);
 758         }
 759 }
 760
 761 /***********************************************************/
 762 int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
 763         try{
 764                 vector< vector< vector<seqDist> > > calcDistsTotals;  //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files
 765         vector< vector<seqDist>  > calcDists; calcDists.resize(treeCalculators.size());
 766
 767         for (int thisIter = 0; thisIter < iters; thisIter++) {
 768
 769             vector<SharedRAbundVector*> thisItersLookup = thisLookup;
 770
 771             if (subsample) {
 772                 SubSample sample;
 773                 vector<string> tempLabels; //dont need since we arent printing the sampled sharedRabunds
 774
 775                 //make copy of lookup so we don't get access violations
 776                 vector<SharedRAbundVector*> newLookup;
 777                 for (int k = 0; k < thisItersLookup.size(); k++) {
 778                     SharedRAbundVector* temp = new SharedRAbundVector();
 779                     temp->setLabel(thisItersLookup[k]->getLabel());
 780                     temp->setGroup(thisItersLookup[k]->getGroup());
 781                     newLookup.push_back(temp);
 782                 }
 783
 784                 //for each bin
 785                 for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
 786                     if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
 787                     for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
 788                 }
 789
 790                 tempLabels = sample.getSample(newLookup, subsampleSize);
 791                 thisItersLookup = newLookup;
 792             }
 793
 794             if(processors == 1){
 795                 driver(thisItersLookup, 0, numGroups, calcDists);
 796             }else{
 797                 int process = 1;
 798                 vector<int> processIDS;
 799
 800 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 801                 //loop through and create all the processes you want
 802                 while (process != processors) {
 803                     pid_t pid = fork();
 804
 805                     if (pid > 0) {
 806                         processIDS.push_back(pid);
 807                         process++;
 808                     }else if (pid == 0){
 809
 810                         driver(thisItersLookup, lines[process].start, lines[process].end, calcDists);
 811
 812                         string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + m->mothurGetpid(process) + ".dist";
 813                         ofstream outtemp;
 814                         m->openOutputFile(tempdistFileName, outtemp);
 815
 816                         for (int i = 0; i < calcDists.size(); i++) {
 817                             outtemp << calcDists[i].size() << endl;
 818
 819                             for (int j = 0; j < calcDists[i].size(); j++) {
 820                                 outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl;
 821                             }
 822                         }
 823                         outtemp.close();
 824
 825                         exit(0);
 826                     }else {
 827                         m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 828                         for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 829                         exit(0);
 830                     }
 831                 }
 832
 833                 //parent do your part
 834                 driver(thisItersLookup, lines[0].start, lines[0].end, calcDists);
 835
 836                 //force parent to wait until all the processes are done
 837                 for (int i = 0; i < processIDS.size(); i++) {
 838                     int temp = processIDS[i];
 839                     wait(&temp);
 840                 }
 841
 842                 for (int i = 0; i < processIDS.size(); i++) {
 843                     string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(processIDS[i]) +  ".dist";
 844                     ifstream intemp;
 845                     m->openInputFile(tempdistFileName, intemp);
 846
 847                     for (int k = 0; k < calcDists.size(); k++) {
 848                         int size = 0;
 849                         intemp >> size; m->gobble(intemp);
 850
 851                         for (int j = 0; j < size; j++) {
 852                             int seq1 = 0;
 853                             int seq2 = 0;
 854                             float dist = 1.0;
 855
 856                             intemp >> seq1 >> seq2 >> dist;   m->gobble(intemp);
 857
 858                             seqDist tempDist(seq1, seq2, dist);
 859                             calcDists[k].push_back(tempDist);
 860                         }
 861                     }
 862                     intemp.close();
 863                     m->mothurRemove(tempdistFileName);
 864                 }
 865 #else
 866                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 867                 //Windows version shared memory, so be careful when passing variables through the treeSharedData struct.
 868                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 869                 //Taking advantage of shared memory to pass results vectors.
 870                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 871
 872                 vector<treeSharedData*> pDataArray;
 873                 DWORD   dwThreadIdArray[processors-1];
 874                 HANDLE  hThreadArray[processors-1];
 875
 876                 //Create processor worker threads.
 877                 for( int i=1; i<processors; i++ ){
 878
 879                     //make copy of lookup so we don't get access violations
 880                     vector<SharedRAbundVector*> newLookup;
 881                     for (int k = 0; k < thisItersLookup.size(); k++) {
 882                         SharedRAbundVector* temp = new SharedRAbundVector();
 883                         temp->setLabel(thisItersLookup[k]->getLabel());
 884                         temp->setGroup(thisItersLookup[k]->getGroup());
 885                         newLookup.push_back(temp);
 886                     }
 887
 888                     //for each bin
 889                     for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
 890                         if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
 891                         for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
 892                     }
 893
 894                     // Allocate memory for thread data.
 895                     treeSharedData* tempSum = new treeSharedData(m, lines[i].start, lines[i].end, Estimators, newLookup);
 896                     pDataArray.push_back(tempSum);
 897                     processIDS.push_back(i);
 898
 899                     hThreadArray[i-1] = CreateThread(NULL, 0, MyTreeSharedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
 900                 }
 901
 902                 //parent do your part
 903                 driver(thisItersLookup, lines[0].start, lines[0].end, calcDists);
 904
 905                 //Wait until all threads have terminated.
 906                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 907
 908                 //Close all thread handles and free memory allocations.
 909                 for(int i=0; i < pDataArray.size(); i++){
 910                     if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) {
 911                         m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " groups assigned to it, quitting. \n"); m->control_pressed = true;
 912                     }
 913                     for (int j = 0; j < pDataArray[i]->thisLookup.size(); j++) {  delete pDataArray[i]->thisLookup[j];  }
 914
 915                     for (int k = 0; k < calcDists.size(); k++) {
 916                         int size = pDataArray[i]->calcDists[k].size();
 917                         for (int j = 0; j < size; j++) {    calcDists[k].push_back(pDataArray[i]->calcDists[k][j]);    }
 918                     }
 919
 920                     CloseHandle(hThreadArray[i]);
 921                     delete pDataArray[i];
 922                 }
 923
 924 #endif
 925             }
 926
 927             calcDistsTotals.push_back(calcDists);
 928
 929             if (subsample) {
 930
 931                 //clean up memory
 932                 for (int i = 0; i < thisItersLookup.size(); i++) { delete thisItersLookup[i]; }
 933                 thisItersLookup.clear();
 934                 for (int i = 0; i < calcDists.size(); i++) {  calcDists[i].clear(); }
 935             }
 936
 937             if (m->debug) {  m->mothurOut("[DEBUG]: iter = " + toString(thisIter) + ".\n"); }
 938                 }
 939
 940                 if (m->debug) {  m->mothurOut("[DEBUG]: done with iters.\n"); }
 941
 942         if (iters != 1) {
 943             //we need to find the average distance and standard deviation for each groups distance
 944             vector< vector<seqDist>  > calcAverages = m->getAverages(calcDistsTotals);
 945
 946             if (m->debug) {  m->mothurOut("[DEBUG]: found averages.\n"); }
 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                 map<string, string> variables;
 965                 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
 966                 variables["[calc]"] = treeCalculators[i]->getName();
 967                 variables["[distance]"] = thisLookup[0]->getLabel();
 968                 variables["[tag]"] = "ave";
 969                 string outputFile = getOutputFileName("tree",variables);
 970                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 971
 972                 //creates tree from similarity matrix and write out file
 973                 Tree* newTree = createTree(matrix);
 974                 if (newTree != NULL) { writeTree(outputFile, newTree); }
 975             }
 976
 977             if (m->debug) {  m->mothurOut("[DEBUG]: done averages trees.\n"); }
 978
 979             //create all trees for each calc and find their consensus tree
 980             for (int i = 0; i < calcDists.size(); i++) {
 981                 if (m->control_pressed) { break; }
 982
 983                 //create a new filename
 984                 //create a new filename
 985                 map<string, string> variables;
 986                 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
 987                 variables["[calc]"] = treeCalculators[i]->getName();
 988                 variables["[distance]"] = thisLookup[0]->getLabel();
 989                 variables["[tag]"] = "all";
 990                 string outputFile = getOutputFileName("tree",variables);
 991                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 992
 993                 ofstream outAll;
 994                 m->openOutputFile(outputFile, outAll);
 995
 996                 vector<Tree*> trees;
 997                 for (int myIter = 0; myIter < iters; myIter++) {
 998
 999                     if(m->control_pressed) { break; }
1000
1001                     //initialize matrix
1002                     vector< vector<double> > matrix; //square matrix to represent the distance
1003                     matrix.resize(thisLookup.size());
1004                     for (int k = 0; k < thisLookup.size(); k++) {  matrix[k].resize(thisLookup.size(), 0.0); }
1005
1006                     for (int j = 0; j < calcDistsTotals[myIter][i].size(); j++) {
1007                         int row = calcDistsTotals[myIter][i][j].seq1;
1008                         int column = calcDistsTotals[myIter][i][j].seq2;
1009                         double dist = calcDistsTotals[myIter][i][j].dist;
1010
1011                         matrix[row][column] = dist;
1012                         matrix[column][row] = dist;
1013                     }
1014
1015                     //creates tree from similarity matrix and write out file
1016                     Tree* newTree = createTree(matrix);
1017                     if (newTree != NULL) {
1018                         newTree->print(outAll);
1019                         trees.push_back(newTree);
1020                     }
1021                 }
1022                 outAll.close();
1023                 if (m->control_pressed) { for (int k = 0; k < trees.size(); k++) { delete trees[k]; } }
1024
1025                 if (m->debug) {  m->mothurOut("[DEBUG]: done all trees.\n"); }
1026
1027                 Consensus consensus;
1028                 //clear old tree names if any
1029                 m->Treenames.clear(); m->Treenames = m->getGroups(); //may have changed if subsample eliminated groups
1030                 Tree* conTree = consensus.getTree(trees);
1031
1032                 if (m->debug) {  m->mothurOut("[DEBUG]: done cons tree.\n"); }
1033
1034                 //create a new filename
1035                 variables["[tag]"] = "cons";
1036                 string conFile = getOutputFileName("tree",variables);
1037                 outputNames.push_back(conFile); outputTypes["tree"].push_back(conFile);
1038                 ofstream outTree;
1039                 m->openOutputFile(conFile, outTree);
1040
1041                 if (conTree != NULL) { conTree->print(outTree, "boot"); delete conTree; }
1042             }
1043
1044         }else {
1045
1046             for (int i = 0; i < calcDists.size(); i++) {
1047                 if (m->control_pressed) { break; }
1048
1049                 //initialize matrix
1050                 vector< vector<double> > matrix; //square matrix to represent the distance
1051                 matrix.resize(thisLookup.size());
1052                 for (int k = 0; k < thisLookup.size(); k++) {  matrix[k].resize(thisLookup.size(), 0.0); }
1053
1054                 for (int j = 0; j < calcDists[i].size(); j++) {
1055                     int row = calcDists[i][j].seq1;
1056                     int column = calcDists[i][j].seq2;
1057                     double dist = calcDists[i][j].dist;
1058
1059                     matrix[row][column] = dist;
1060                     matrix[column][row] = dist;
1061                 }
1062
1063                 //create a new filename
1064                 map<string, string> variables;
1065                 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
1066                 variables["[calc]"] = treeCalculators[i]->getName();
1067                 variables["[distance]"] = thisLookup[0]->getLabel();
1068                 variables["[tag]"] = "";
1069                 string outputFile = getOutputFileName("tree",variables);
1070                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
1071
1072                 //creates tree from similarity matrix and write out file
1073                 Tree* newTree = createTree(matrix);
1074                 if (newTree != NULL) { writeTree(outputFile, newTree); delete newTree; }
1075             }
1076         }
1077
1078                 return 0;
1079         }
1080         catch(exception& e) {
1081                 m->errorOut(e, "TreeGroupCommand", "process");
1082                 exit(1);
1083         }
1084 }
1085 /**************************************************************************************************/
1086 int TreeGroupCommand::driver(vector<SharedRAbundVector*> thisLookup, int start, int end, vector< vector<seqDist> >& calcDists) {
1087         try {
1088                 vector<SharedRAbundVector*> subset;
1089                 for (int k = start; k < end; k++) { // pass cdd each set of groups to compare
1090
1091                         for (int l = 0; l < k; l++) {
1092
1093                                 if (k != l) { //we dont need to similiarity of a groups to itself
1094                                         subset.clear(); //clear out old pair of sharedrabunds
1095                                         //add new pair of sharedrabunds
1096                                         subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
1097
1098                                         for(int i=0;i<treeCalculators.size();i++) {
1099
1100                                                 //if this calc needs all groups to calculate the pair load all groups
1101                                                 if (treeCalculators[i]->getNeedsAll()) {
1102                                                         //load subset with rest of lookup for those calcs that need everyone to calc for a pair
1103                                                         for (int w = 0; w < thisLookup.size(); w++) {
1104                                                                 if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
1105                                                         }
1106                                                 }
1107
1108                                                 vector<double> tempdata = treeCalculators[i]->getValues(subset); //saves the calculator outputs
1109
1110                                                 if (m->control_pressed) { return 1; }
1111
1112                                                 seqDist temp(l, k, -(tempdata[0]-1.0));
1113                                                 calcDists[i].push_back(temp);
1114                                         }
1115                                 }
1116                         }
1117                 }
1118
1119                 return 0;
1120         }
1121         catch(exception& e) {
1122                 m->errorOut(e, "TreeGroupCommand", "driver");
1123                 exit(1);
1124         }
1125 }
1126 /***********************************************************/
1127
1128
1129