treegroupscommand.cpp

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