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