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 "sharedsobscollectsummary.h"
  12 #include "sharedchao1.h"
  13 #include "sharedace.h"
  14 #include "sharednseqs.h"
  15 #include "sharedjabund.h"
  16 #include "sharedsorabund.h"
  17 #include "sharedjclass.h"
  18 #include "sharedsorclass.h"
  19 #include "sharedjest.h"
  20 #include "sharedsorest.h"
  21 #include "sharedthetayc.h"
  22 #include "sharedthetan.h"
  23 #include "sharedkstest.h"
  24 #include "whittaker.h"
  25 #include "sharedochiai.h"
  26 #include "sharedanderbergs.h"
  27 #include "sharedkulczynski.h"
  28 #include "sharedkulczynskicody.h"
  29 #include "sharedlennon.h"
  30 #include "sharedmorisitahorn.h"
  31 #include "sharedbraycurtis.h"
  32 #include "sharedjackknife.h"
  33 #include "whittaker.h"
  34 #include "odum.h"
  35 #include "canberra.h"
  36 #include "structeuclidean.h"
  37 #include "structchord.h"
  38 #include "hellinger.h"
  39 #include "manhattan.h"
  40 #include "structpearson.h"
  41 #include "soergel.h"
  42 #include "spearman.h"
  43 #include "structkulczynski.h"
  44 #include "structchi2.h"
  45 #include "speciesprofile.h"
  46 #include "hamming.h"
  47 #include "gower.h"
  48 #include "memchi2.h"
  49 #include "memchord.h"
  50 #include "memeuclidean.h"
  51 #include "mempearson.h"
  52
  53 //**********************************************************************************************************************
  54 vector<string> TreeGroupCommand::setParameters(){
  55         try {
  56                 CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);
  57                 CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
  58                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
  59                 CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn);
  60                 CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
  61                 CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
  62                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  63                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  64                 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);
  65                 CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
  66                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  67                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  68
  69                 vector<string> myArray;
  70                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  71                 return myArray;
  72         }
  73         catch(exception& e) {
  74                 m->errorOut(e, "TreeGroupCommand", "setParameters");
  75                 exit(1);
  76         }
  77 }
  78 //**********************************************************************************************************************
  79 string TreeGroupCommand::getHelpString(){
  80         try {
  81                 string helpString = "";
  82                 ValidCalculators validCalculator;
  83                 helpString += "The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n";
  84                 helpString += "The tree.shared command parameters are shared, groups, calc, phylip, column, name, cutoff, precision and label.\n";
  85                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
  86                 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";
  87                 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";
  88                 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";
  89                 helpString += "The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
  90                 helpString += "Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n";
  91                 helpString += "The default value for groups is all the groups in your groupfile.\n";
  92                 helpString += "The default value for calc is jclass-thetayc.\n";
  93                 helpString += "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n";
  94                 helpString += validCalculator.printCalc("treegroup");
  95                 helpString += "Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n";
  96                 helpString += "Example tree.shared(phylip=abrecovery.dist).\n";
  97                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
  98                 return helpString;
  99         }
 100         catch(exception& e) {
 101                 m->errorOut(e, "TreeGroupCommand", "getHelpString");
 102                 exit(1);
 103         }
 104 }
 105 //**********************************************************************************************************************
 106 TreeGroupCommand::TreeGroupCommand(){
 107         try {
 108                 abort = true; calledHelp = true;
 109                 setParameters();
 110                 //initialize outputTypes
 111                 vector<string> tempOutNames;
 112                 outputTypes["tree"] = tempOutNames;
 113         }
 114         catch(exception& e) {
 115                 m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
 116                 exit(1);
 117         }
 118 }
 119 //**********************************************************************************************************************
 120
 121 TreeGroupCommand::TreeGroupCommand(string option)  {
 122         try {
 123                 abort = false; calledHelp = false;
 124                 allLines = 1;
 125
 126                 //allow user to run help
 127                 if(option == "help") { help(); abort = true; calledHelp = true; }
 128
 129                 else {
 130                         vector<string> myArray = setParameters();
 131
 132                         OptionParser parser(option);
 133                         map<string, string> parameters = parser. getParameters();
 134
 135                         ValidParameters validParameter;
 136                         map<string, string>::iterator it;
 137
 138                         //check to make sure all parameters are valid for command
 139                         for (it = parameters.begin(); it != parameters.end(); it++) {
 140                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 141                         }
 142
 143                         //initialize outputTypes
 144                         vector<string> tempOutNames;
 145                         outputTypes["tree"] = tempOutNames;
 146
 147                         //if the user changes the input directory command factory will send this info to us in the output parameter
 148                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 149                         if (inputDir == "not found"){   inputDir = "";          }
 150                         else {
 151                                 string path;
 152                                 it = parameters.find("phylip");
 153                                 //user has given a template file
 154                                 if(it != parameters.end()){
 155                                         path = m->hasPath(it->second);
 156                                         //if the user has not given a path then, add inputdir. else leave path alone.
 157                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 158                                 }
 159
 160                                 it = parameters.find("column");
 161                                 //user has given a template file
 162                                 if(it != parameters.end()){
 163                                         path = m->hasPath(it->second);
 164                                         //if the user has not given a path then, add inputdir. else leave path alone.
 165                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
 166                                 }
 167
 168                                 it = parameters.find("name");
 169                                 //user has given a template file
 170                                 if(it != parameters.end()){
 171                                         path = m->hasPath(it->second);
 172                                         //if the user has not given a path then, add inputdir. else leave path alone.
 173                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 174                                 }
 175                         }
 176
 177                         //check for required parameters
 178                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 179                         if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 180                         else if (phylipfile == "not found") { phylipfile = ""; }
 181                         else {  inputfile = phylipfile;  format = "phylip";     }
 182
 183                         columnfile = validParameter.validFile(parameters, "column", true);
 184                         if (columnfile == "not open") { columnfile = ""; abort = true; }
 185                         else if (columnfile == "not found") { columnfile = ""; }
 186                         else {  inputfile = columnfile; format = "column";      }
 187
 188                         sharedfile = validParameter.validFile(parameters, "shared", true);
 189                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 190                         else if (sharedfile == "not found") { sharedfile = ""; }
 191                         else {  inputfile = sharedfile; format = "sharedfile";  }
 192
 193                         namefile = validParameter.validFile(parameters, "name", true);
 194                         if (namefile == "not open") { abort = true; }
 195                         else if (namefile == "not found") { namefile = ""; }
 196
 197                         if ((phylipfile == "") && (columnfile == "") && (sharedfile == "")) {
 198                                 //is there are current file available for either of these?
 199                                 //give priority to shared, then column, then phylip
 200                                 sharedfile = m->getSharedFile();
 201                                 if (sharedfile != "") {  inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 202                                 else {
 203                                         columnfile = m->getColumnFile();
 204                                         if (columnfile != "") { inputfile = columnfile; format = "column";  m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
 205                                         else {
 206                                                 phylipfile = m->getPhylipFile();
 207                                                 if (phylipfile != "") { inputfile = phylipfile;  format = "phylip";  m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 208                                                 else {
 209                                                         m->mothurOut("No valid current files. You must provide a shared, phylip or column file."); m->mothurOutEndLine();
 210                                                         abort = true;
 211                                                 }
 212                                         }
 213                                 }
 214                         }
 215                         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; }
 216
 217                         if (columnfile != "") {
 218                                 if (namefile == "") {
 219                                         namefile = m->getNameFile();
 220                                         if (namefile != "") {  m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
 221                                         else {
 222                                                 m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine();
 223                                                 abort = true;
 224                                         }
 225                                 }
 226                         }
 227
 228                         //check for optional parameter and set defaults
 229                         // ...at some point should added some additional type checking...
 230                         label = validParameter.validFile(parameters, "label", false);
 231                         if (label == "not found") { label = ""; }
 232                         else {
 233                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 234                                 else { allLines = 1;  }
 235                         }
 236
 237                         groups = validParameter.validFile(parameters, "groups", false);
 238                         if (groups == "not found") { groups = ""; }
 239                         else {
 240                                 m->splitAtDash(groups, Groups);
 241                                 m->Groups = Groups;
 242                         }
 243
 244                         calc = validParameter.validFile(parameters, "calc", false);
 245                         if (calc == "not found") { calc = "jclass-thetayc";  }
 246                         else {
 247                                  if (calc == "default")  {  calc = "jclass-thetayc";  }
 248                         }
 249                         m->splitAtDash(calc, Estimators);
 250
 251                         string temp;
 252                         temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }
 253                         convert(temp, precision);
 254
 255                         temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10"; }
 256                         convert(temp, cutoff);
 257                         cutoff += (5 / (precision * 10.0));
 258
 259                         //if the user changes the output directory command factory will send this info to us in the output parameter
 260                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 261                                 outputDir = "";
 262                                 outputDir += m->hasPath(inputfile); //if user entered a file with a path then preserve it
 263                         }
 264                 }
 265
 266         }
 267         catch(exception& e) {
 268                 m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
 269                 exit(1);
 270         }
 271 }
 272 //**********************************************************************************************************************
 273
 274 TreeGroupCommand::~TreeGroupCommand(){
 275         if (abort == false) {
 276                 if (format == "sharedfile") {  delete input; }
 277                 else { delete readMatrix;  delete matrix; delete list; }
 278                 delete tmap;
 279         }
 280
 281 }
 282
 283 //**********************************************************************************************************************
 284
 285 int TreeGroupCommand::execute(){
 286         try {
 287
 288                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 289
 290                 if (format == "sharedfile") {
 291
 292                         ValidCalculators validCalculator;
 293
 294                         for (int i=0; i<Estimators.size(); i++) {
 295                                 if (validCalculator.isValidCalculator("treegroup", Estimators[i]) == true) {
 296                                         if (Estimators[i] == "sharedsobs") {
 297                                                 treeCalculators.push_back(new SharedSobsCS());
 298                                         }else if (Estimators[i] == "sharedchao") {
 299                                                 treeCalculators.push_back(new SharedChao1());
 300                                         }else if (Estimators[i] == "sharedace") {
 301                                                 treeCalculators.push_back(new SharedAce());
 302                                         }else if (Estimators[i] == "jabund") {
 303                                                 treeCalculators.push_back(new JAbund());
 304                                         }else if (Estimators[i] == "sorabund") {
 305                                                 treeCalculators.push_back(new SorAbund());
 306                                         }else if (Estimators[i] == "jclass") {
 307                                                 treeCalculators.push_back(new Jclass());
 308                                         }else if (Estimators[i] == "sorclass") {
 309                                                 treeCalculators.push_back(new SorClass());
 310                                         }else if (Estimators[i] == "jest") {
 311                                                 treeCalculators.push_back(new Jest());
 312                                         }else if (Estimators[i] == "sorest") {
 313                                                 treeCalculators.push_back(new SorEst());
 314                                         }else if (Estimators[i] == "thetayc") {
 315                                                 treeCalculators.push_back(new ThetaYC());
 316                                         }else if (Estimators[i] == "thetan") {
 317                                                 treeCalculators.push_back(new ThetaN());
 318                                         }else if (Estimators[i] == "kstest") {
 319                                                 treeCalculators.push_back(new KSTest());
 320                                         }else if (Estimators[i] == "sharednseqs") {
 321                                                 treeCalculators.push_back(new SharedNSeqs());
 322                                         }else if (Estimators[i] == "ochiai") {
 323                                                 treeCalculators.push_back(new Ochiai());
 324                                         }else if (Estimators[i] == "anderberg") {
 325                                                 treeCalculators.push_back(new Anderberg());
 326                                         }else if (Estimators[i] == "kulczynski") {
 327                                                 treeCalculators.push_back(new Kulczynski());
 328                                         }else if (Estimators[i] == "kulczynskicody") {
 329                                                 treeCalculators.push_back(new KulczynskiCody());
 330                                         }else if (Estimators[i] == "lennon") {
 331                                                 treeCalculators.push_back(new Lennon());
 332                                         }else if (Estimators[i] == "morisitahorn") {
 333                                                 treeCalculators.push_back(new MorHorn());
 334                                         }else if (Estimators[i] == "braycurtis") {
 335                                                 treeCalculators.push_back(new BrayCurtis());
 336                                         }else if (Estimators[i] == "whittaker") {
 337                                                 treeCalculators.push_back(new Whittaker());
 338                                         }else if (Estimators[i] == "odum") {
 339                                                 treeCalculators.push_back(new Odum());
 340                                         }else if (Estimators[i] == "canberra") {
 341                                                 treeCalculators.push_back(new Canberra());
 342                                         }else if (Estimators[i] == "structeuclidean") {
 343                                                 treeCalculators.push_back(new StructEuclidean());
 344                                         }else if (Estimators[i] == "structchord") {
 345                                                 treeCalculators.push_back(new StructChord());
 346                                         }else if (Estimators[i] == "hellinger") {
 347                                                 treeCalculators.push_back(new Hellinger());
 348                                         }else if (Estimators[i] == "manhattan") {
 349                                                 treeCalculators.push_back(new Manhattan());
 350                                         }else if (Estimators[i] == "structpearson") {
 351                                                 treeCalculators.push_back(new StructPearson());
 352                                         }else if (Estimators[i] == "soergel") {
 353                                                 treeCalculators.push_back(new Soergel());
 354                                         }else if (Estimators[i] == "spearman") {
 355                                                 treeCalculators.push_back(new Spearman());
 356                                         }else if (Estimators[i] == "structkulczynski") {
 357                                                 treeCalculators.push_back(new StructKulczynski());
 358                                         }else if (Estimators[i] == "speciesprofile") {
 359                                                 treeCalculators.push_back(new SpeciesProfile());
 360                                         }else if (Estimators[i] == "hamming") {
 361                                                 treeCalculators.push_back(new Hamming());
 362                                         }else if (Estimators[i] == "structchi2") {
 363                                                 treeCalculators.push_back(new StructChi2());
 364                                         }else if (Estimators[i] == "gower") {
 365                                                 treeCalculators.push_back(new Gower());
 366                                         }else if (Estimators[i] == "memchi2") {
 367                                                 treeCalculators.push_back(new MemChi2());
 368                                         }else if (Estimators[i] == "memchord") {
 369                                                 treeCalculators.push_back(new MemChord());
 370                                         }else if (Estimators[i] == "memeuclidean") {
 371                                                 treeCalculators.push_back(new MemEuclidean());
 372                                         }else if (Estimators[i] == "mempearson") {
 373                                                 treeCalculators.push_back(new MemPearson());
 374                                         }
 375                                 }
 376                         }
 377
 378                         //if the users entered no valid calculators don't execute command
 379                         if (treeCalculators.size() == 0) { m->mothurOut("You have given no valid calculators."); m->mothurOutEndLine(); return 0; }
 380
 381                         input = new InputData(sharedfile, "sharedfile");
 382                         lookup = input->getSharedRAbundVectors();
 383                         lastLabel = lookup[0]->getLabel();
 384
 385                         if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); return 0; }
 386
 387                         //used in tree constructor
 388                         m->runParse = false;
 389
 390                         //create treemap class from groupmap for tree class to use
 391                         tmap = new TreeMap();
 392                         tmap->makeSim(m->namesOfGroups);
 393
 394                         //clear globaldatas old tree names if any
 395                         m->Treenames.clear();
 396
 397                         //fills globaldatas tree names
 398                         m->Treenames = m->Groups;
 399
 400                         if (m->control_pressed) { return 0; }
 401
 402                         //create tree file
 403                         makeSimsShared();
 404
 405                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
 406                 }else{
 407                         //read in dist file
 408                         filename = inputfile;
 409
 410                         if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
 411                         else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
 412
 413                         readMatrix->setCutoff(cutoff);
 414
 415                         if(namefile != ""){
 416                                 nameMap = new NameAssignment(namefile);
 417                                 nameMap->readMap();
 418                         }
 419                         else{
 420                                 nameMap = NULL;
 421                         }
 422
 423                         readMatrix->read(nameMap);
 424                         list = readMatrix->getListVector();
 425                         matrix = readMatrix->getMatrix();
 426
 427                         //make treemap
 428                         tmap = new TreeMap();
 429
 430                         if (m->control_pressed) { return 0; }
 431
 432                         tmap->makeSim(list);
 433
 434                         m->Groups = tmap->namesOfGroups;
 435
 436                         //clear globaldatas old tree names if any
 437                         m->Treenames.clear();
 438
 439                         //fills globaldatas tree names
 440                         m->Treenames = m->Groups;
 441
 442                         //used in tree constructor
 443                         m->runParse = false;
 444
 445                         if (m->control_pressed) { return 0; }
 446
 447                         makeSimsDist();
 448
 449                         if (m->control_pressed) { return 0; }
 450
 451                         //create a new filename
 452                         outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "tre";
 453                         outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 454
 455                         createTree();
 456
 457                         if (m->control_pressed) { return 0; }
 458
 459                         m->mothurOut("Tree complete. "); m->mothurOutEndLine();
 460
 461                 }
 462
 463                 //reset groups parameter
 464                 m->Groups.clear();
 465
 466                 //set tree file as new current treefile
 467                 string current = "";
 468                 itTypes = outputTypes.find("tree");
 469                 if (itTypes != outputTypes.end()) {
 470                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
 471                 }
 472
 473                 m->mothurOutEndLine();
 474                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 475                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 476                 m->mothurOutEndLine();
 477
 478                 return 0;
 479         }
 480         catch(exception& e) {
 481                 m->errorOut(e, "TreeGroupCommand", "execute");
 482                 exit(1);
 483         }
 484 }
 485 //**********************************************************************************************************************
 486
 487 int TreeGroupCommand::createTree(){
 488         try {
 489                 //create tree
 490                 t = new Tree(tmap);
 491
 492                 //do merges and create tree structure by setting parents and children
 493                 //there are numGroups - 1 merges to do
 494                 for (int i = 0; i < (numGroups - 1); i++) {
 495                         float largest = -1000.0;
 496
 497                         if (m->control_pressed) { delete t; return 1; }
 498
 499                         int row, column;
 500                         //find largest value in sims matrix by searching lower triangle
 501                         for (int j = 1; j < simMatrix.size(); j++) {
 502                                 for (int k = 0; k < j; k++) {
 503                                         if (simMatrix[j][k] > largest) {  largest = simMatrix[j][k]; row = j; column = k;  }
 504                                 }
 505                         }
 506
 507                         //set non-leaf node info and update leaves to know their parents
 508                         //non-leaf
 509                         t->tree[numGroups + i].setChildren(index[row], index[column]);
 510
 511                         //parents
 512                         t->tree[index[row]].setParent(numGroups + i);
 513                         t->tree[index[column]].setParent(numGroups + i);
 514
 515                         //blength = distance / 2;
 516                         float blength = ((1.0 - largest) / 2);
 517
 518                         //branchlengths
 519                         t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
 520                         t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
 521
 522                         //set your length to leaves to your childs length plus branchlength
 523                         t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
 524
 525
 526                         //update index
 527                         index[row] = numGroups+i;
 528                         index[column] = numGroups+i;
 529
 530                         //remove highest value that caused the merge.
 531                         simMatrix[row][column] = -1000.0;
 532                         simMatrix[column][row] = -1000.0;
 533
 534                         //merge values in simsMatrix
 535                         for (int n = 0; n < simMatrix.size(); n++)      {
 536                                 //row becomes merge of 2 groups
 537                                 simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
 538                                 simMatrix[n][row] = simMatrix[row][n];
 539                                 //delete column
 540                                 simMatrix[column][n] = -1000.0;
 541                                 simMatrix[n][column] = -1000.0;
 542                         }
 543                 }
 544
 545                 //adjust tree to make sure root to tip length is .5
 546                 int root = t->findRoot();
 547                 t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves()));
 548
 549                 //assemble tree
 550                 t->assembleTree();
 551
 552                 if (m->control_pressed) { delete t; return 1; }
 553
 554                 //print newick file
 555                 t->createNewickFile(outputFile);
 556
 557                 //delete tree
 558                 delete t;
 559
 560                 if (m->control_pressed) { remove(outputFile.c_str()); outputNames.pop_back(); return 1; }
 561
 562                 return 0;
 563
 564         }
 565         catch(exception& e) {
 566                 m->errorOut(e, "TreeGroupCommand", "createTree");
 567                 exit(1);
 568         }
 569 }
 570 /***********************************************************/
 571 void TreeGroupCommand::printSims(ostream& out) {
 572         try {
 573
 574                 //output column headers
 575                 //out << '\t';
 576                 //for (int i = 0; i < lookup.size(); i++) {     out << lookup[i]->getGroup() << '\t';           }
 577                 //out << endl;
 578
 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 int TreeGroupCommand::makeSimsDist() {
 596         try {
 597                 numGroups = list->size();
 598
 599                 //initialize index
 600                 index.clear();
 601                 for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 602
 603                 //initialize simMatrix
 604                 simMatrix.clear();
 605                 simMatrix.resize(numGroups);
 606                 for (int k = 0; k < simMatrix.size(); k++)      {
 607                         for (int j = 0; j < simMatrix.size(); j++)      {
 608                                 simMatrix[k].push_back(0.0);
 609                         }
 610                 }
 611
 612                 //go through sparse matrix and fill sims
 613                 //go through each cell in the sparsematrix
 614                 for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
 615                         //similairity = -(distance-1)
 616                         simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0);
 617                         simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);
 618
 619                         if (m->control_pressed) { return 1; }
 620
 621                 }
 622
 623                 return 0;
 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                 set<string> processedLabels;
 635                 set<string> userLabels = labels;
 636
 637                 //as long as you are not at the end of the file or done wih the lines you want
 638                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 639                         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; }
 640
 641                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 642                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 643                                 process(lookup);
 644
 645                                 processedLabels.insert(lookup[0]->getLabel());
 646                                 userLabels.erase(lookup[0]->getLabel());
 647                         }
 648
 649                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 650                                 string saveLabel = lookup[0]->getLabel();
 651
 652                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 653                                 lookup = input->getSharedRAbundVectors(lastLabel);
 654
 655                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 656                                 process(lookup);
 657
 658                                 processedLabels.insert(lookup[0]->getLabel());
 659                                 userLabels.erase(lookup[0]->getLabel());
 660
 661                                 //restore real lastlabel to save below
 662                                 lookup[0]->setLabel(saveLabel);
 663                         }
 664
 665                         lastLabel = lookup[0]->getLabel();
 666
 667                         //get next line to process
 668                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 669                         lookup = input->getSharedRAbundVectors();
 670                 }
 671
 672                 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; }
 673
 674                 //output error messages about any remaining user labels
 675                 set<string>::iterator it;
 676                 bool needToRun = false;
 677                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 678                         m->mothurOut("Your file does not include the label " + *it);
 679                         if (processedLabels.count(lastLabel) != 1) {
 680                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 681                                 needToRun = true;
 682                         }else {
 683                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 684                         }
 685                 }
 686
 687                 //run last label if you need to
 688                 if (needToRun == true)  {
 689                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {             delete lookup[i]; }             }
 690                         lookup = input->getSharedRAbundVectors(lastLabel);
 691
 692                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 693                         process(lookup);
 694                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 695                 }
 696
 697                 for(int i = 0 ; i < treeCalculators.size(); i++) {  delete treeCalculators[i]; }
 698
 699                 return 0;
 700         }
 701         catch(exception& e) {
 702                 m->errorOut(e, "TreeGroupCommand", "makeSimsShared");
 703                 exit(1);
 704         }
 705 }
 706
 707 /***********************************************************/
 708 int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
 709         try{
 710                                 EstOutput data;
 711                                 vector<SharedRAbundVector*> subset;
 712                                 numGroups = thisLookup.size();
 713
 714                                 //for each calculator
 715                                 for(int i = 0 ; i < treeCalculators.size(); i++) {
 716                                         //initialize simMatrix
 717                                         simMatrix.clear();
 718                                         simMatrix.resize(numGroups);
 719                                         for (int k = 0; k < simMatrix.size(); k++)      {
 720                                                 for (int j = 0; j < simMatrix.size(); j++)      {
 721                                                         simMatrix[k].push_back(0.0);
 722                                                 }
 723                                         }
 724
 725                                         //initialize index
 726                                         index.clear();
 727                                         for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 728
 729                                         //create a new filename
 730                                         outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
 731                                         outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 732
 733                                         for (int k = 0; k < thisLookup.size(); k++) {
 734                                                 for (int l = k; l < thisLookup.size(); l++) {
 735                                                         if (k != l) { //we dont need to similiarity of a groups to itself
 736                                                                 //get estimated similarity between 2 groups
 737
 738                                                                 subset.clear(); //clear out old pair of sharedrabunds
 739                                                                 //add new pair of sharedrabunds
 740                                                                 subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
 741
 742                                                                 //if this calc needs all groups to calculate the pair load all groups
 743                                                                 if (treeCalculators[i]->getNeedsAll()) {
 744                                                                         //load subset with rest of lookup for those calcs that need everyone to calc for a pair
 745                                                                         for (int w = 0; w < thisLookup.size(); w++) {
 746                                                                                 if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
 747                                                                         }
 748                                                                 }
 749
 750                                                                 data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
 751                                                 //cout << thisLookup[k]->getGroup() << '\t' << thisLookup[l]->getGroup() << '\t' << (1.0 - data[0]) << endl;
 752                                                                 if (m->control_pressed) { return 1; }
 753
 754                                                                 //save values in similarity matrix
 755                                                                 simMatrix[k][l] = data[0];
 756                                                                 simMatrix[l][k] = data[0];
 757                                                         }
 758                                                 }
 759                                         }
 760
 761                                         //createdistance file from simMatrix
 762                                         /*string o = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist";
 763                                         ofstream outDist;
 764                                         m->openOutputFile(o, outDist);
 765                                         outDist << simMatrix.size() << endl;
 766                                         for (int k = 0; k < simMatrix.size(); k++) {
 767                                                 outDist << thisLookup[k]->getGroup() << '\t';
 768                                                 for (int l = 0; l < k; l++) {
 769                                                         outDist << (1.0-simMatrix[k][l]) << '\t';
 770                                                 }
 771                                                 outDist << endl;
 772                                         }
 773                                         outDist.close();*/
 774
 775
 776                                         if (m->control_pressed) { return 1; }
 777                                         //creates tree from similarity matrix and write out file
 778                                         createTree();
 779
 780                                         if (m->control_pressed) { return 1; }
 781                                 }
 782
 783                                 return 0;
 784
 785         }
 786         catch(exception& e) {
 787                 m->errorOut(e, "TreeGroupCommand", "process");
 788                 exit(1);
 789         }
 790 }
 791 /***********************************************************/
 792
 793
 794