parsimonycommand.cpp

   1 /*
   2  *  parsimonycommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 1/26/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "parsimonycommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> ParsimonyCommand::setParameters(){
  14         try {
  15                 CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
  16                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
  17                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  18                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  19                 CommandParameter prandom("random", "String", "", "", "", "", "",false,false); parameters.push_back(prandom);
  20                 CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
  21                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  22                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  23                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  24
  25                 vector<string> myArray;
  26                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  27                 return myArray;
  28         }
  29         catch(exception& e) {
  30                 m->errorOut(e, "ParsimonyCommand", "setParameters");
  31                 exit(1);
  32         }
  33 }
  34 //**********************************************************************************************************************
  35 string ParsimonyCommand::getHelpString(){
  36         try {
  37                 string helpString = "";
  38                 helpString += "The parsimony command parameters are tree, group, name, random, groups, processors and iters.  tree parameter is required unless you have valid current tree file or are using random.\n";
  39                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 1 valid group.\n";
  40                 helpString += "The group names are separated by dashes.  The iters parameter allows you to specify how many random trees you would like compared to your tree.\n";
  41                 helpString += "The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters).\n";
  42                 helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
  43                 helpString += "Example parsimony(random=out, iters=500).\n";
  44                 helpString += "The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony),\n";
  45                 helpString += "and iters is 1000.  The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n";
  46                 helpString += "Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n";
  47                 return helpString;
  48         }
  49         catch(exception& e) {
  50                 m->errorOut(e, "ParsimonyCommand", "getHelpString");
  51                 exit(1);
  52         }
  53 }
  54
  55 //**********************************************************************************************************************
  56 ParsimonyCommand::ParsimonyCommand(){
  57         try {
  58                 abort = true; calledHelp = true;
  59                 setParameters();
  60                 vector<string> tempOutNames;
  61                 outputTypes["parsimony"] = tempOutNames;
  62                 outputTypes["psummary"] = tempOutNames;
  63         }
  64         catch(exception& e) {
  65                 m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand");
  66                 exit(1);
  67         }
  68 }
  69 /***********************************************************/
  70 ParsimonyCommand::ParsimonyCommand(string option)  {
  71         try {
  72                 abort = false; calledHelp = false;
  73                 Groups.clear();
  74
  75                 //allow user to run help
  76                 if(option == "help") { help(); abort = true; calledHelp = true; }
  77
  78                 else {
  79                         vector<string> myArray = setParameters();
  80
  81                         OptionParser parser(option);
  82                         map<string, string> parameters = parser.getParameters();
  83                         map<string,string>::iterator it;
  84
  85                         ValidParameters validParameter;
  86
  87                         //check to make sure all parameters are valid for command
  88                         for (it = parameters.begin(); it != parameters.end(); it++) {
  89                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  90                         }
  91
  92                         //initialize outputTypes
  93                         vector<string> tempOutNames;
  94                         outputTypes["parsimony"] = tempOutNames;
  95                         outputTypes["psummary"] = tempOutNames;
  96
  97                         //if the user changes the input directory command factory will send this info to us in the output parameter
  98                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  99                         if (inputDir == "not found"){   inputDir = "";          }
 100                         else {
 101                                 string path;
 102                                 it = parameters.find("tree");
 103                                 //user has given a template file
 104                                 if(it != parameters.end()){
 105                                         path = m->hasPath(it->second);
 106                                         //if the user has not given a path then, add inputdir. else leave path alone.
 107                                         if (path == "") {       parameters["tree"] = inputDir + it->second;             }
 108                                 }
 109
 110                                 it = parameters.find("group");
 111                                 //user has given a template file
 112                                 if(it != parameters.end()){
 113                                         path = m->hasPath(it->second);
 114                                         //if the user has not given a path then, add inputdir. else leave path alone.
 115                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 116                                 }
 117
 118                                 it = parameters.find("name");
 119                                 //user has given a template file
 120                                 if(it != parameters.end()){
 121                                         path = m->hasPath(it->second);
 122                                         //if the user has not given a path then, add inputdir. else leave path alone.
 123                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 124                                 }
 125                         }
 126
 127                         m->runParse = true;
 128
 129                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 130
 131                         randomtree = validParameter.validFile(parameters, "random", false);             if (randomtree == "not found") { randomtree = ""; }
 132
 133                         //are you trying to use parsimony without reading a tree or saying you want random distribution
 134                         if (randomtree == "")  {
 135                                 //check for required parameters
 136                                 treefile = validParameter.validFile(parameters, "tree", true);
 137                                 if (treefile == "not open") { abort = true; }
 138                                 else if (treefile == "not found") {                             //if there is a current design file, use it
 139                                         treefile = m->getTreeFile();
 140                                         if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
 141                                         else {  m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
 142                                 }
 143
 144                                 //check for required parameters
 145                                 groupfile = validParameter.validFile(parameters, "group", true);
 146                                 if (groupfile == "not open") { abort = true; }
 147                                 else if (groupfile == "not found") { groupfile = ""; }
 148
 149                                 namefile = validParameter.validFile(parameters, "name", true);
 150                                 if (namefile == "not open") { abort = true; }
 151                                 else if (namefile == "not found") { namefile = ""; }
 152                         }
 153
 154                         //if the user changes the output directory command factory will send this info to us in the output parameter
 155                         string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found"){  outputDir = ""; if (randomtree == "")  { outputDir += m->hasPath(treefile); } }
 156
 157                         //check for optional parameter and set defaults
 158                         // ...at some point should added some additional type checking...
 159                         groups = validParameter.validFile(parameters, "groups", false);
 160                         if (groups == "not found") { groups = ""; m->Groups.clear(); }
 161                         else {
 162                                 m->splitAtDash(groups, Groups);
 163                                 m->Groups = Groups;
 164                         }
 165
 166                         itersString = validParameter.validFile(parameters, "iters", false);                     if (itersString == "not found") { itersString = "1000"; }
 167                         convert(itersString, iters);
 168
 169                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 170                         m->setProcessors(temp);
 171                         convert(temp, processors);
 172
 173                 }
 174
 175         }
 176         catch(exception& e) {
 177                 m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand");
 178                 exit(1);
 179         }
 180 }
 181 /***********************************************************/
 182 int ParsimonyCommand::execute() {
 183         try {
 184
 185                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 186
 187
 188                 //randomtree will tell us if user had their own treefile or if they just want the random distribution
 189                 //user has entered their own tree
 190                 if (randomtree == "") {
 191                         if (groupfile != "") {
 192                                 //read in group map info.
 193                                 tmap = new TreeMap(groupfile);
 194                                 tmap->readMap();
 195                         }else{ //fake out by putting everyone in one group
 196                                 Tree* tree = new Tree(treefile); delete tree;  //extracts names from tree to make faked out groupmap
 197                                 tmap = new TreeMap();
 198
 199                                 for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
 200                         }
 201
 202                         if (namefile != "") { readNamesFile(); }
 203
 204                         read = new ReadNewickTree(treefile);
 205                         int readOk = read->read(tmap);
 206
 207                         if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete tmap; delete read; return 0; }
 208
 209                         read->AssembleTrees();
 210                         T = read->getTrees();
 211                         delete read;
 212
 213                         //make sure all files match
 214                         //if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
 215                         int numNamesInTree;
 216                         if (namefile != "")  {
 217                                 if (numUniquesInName == m->Treenames.size()) {  numNamesInTree = nameMap.size();  }
 218                                 else {   numNamesInTree = m->Treenames.size();  }
 219                         }else {  numNamesInTree = m->Treenames.size();  }
 220
 221
 222                         //output any names that are in group file but not in tree
 223                         if (numNamesInTree < tmap->getNumSeqs()) {
 224                                 for (int i = 0; i < tmap->namesOfSeqs.size(); i++) {
 225                                         //is that name in the tree?
 226                                         int count = 0;
 227                                         for (int j = 0; j < m->Treenames.size(); j++) {
 228                                                 if (tmap->namesOfSeqs[i] == m->Treenames[j]) { break; } //found it
 229                                                 count++;
 230                                         }
 231
 232                                         if (m->control_pressed) {
 233                                                 delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 234                                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
 235                                                 m->Groups.clear();
 236                                                 return 0;
 237                                         }
 238
 239                                         //then you did not find it so report it
 240                                         if (count == m->Treenames.size()) {
 241                                                 //if it is in your namefile then don't remove
 242                                                 map<string, string>::iterator it = nameMap.find(tmap->namesOfSeqs[i]);
 243
 244                                                 if (it == nameMap.end()) {
 245                                                         m->mothurOut(tmap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
 246                                                         tmap->removeSeq(tmap->namesOfSeqs[i]);
 247                                                         i--; //need this because removeSeq removes name from namesOfSeqs
 248                                                 }
 249                                         }
 250                                 }
 251                         }
 252
 253                         if(outputDir == "") { outputDir += m->hasPath(treefile); }
 254                         output = new ColumnFile(outputDir + m->getSimpleName(treefile)  +  ".parsimony", itersString);
 255                         outputNames.push_back(outputDir + m->getSimpleName(treefile)  +  ".parsimony");
 256                         outputTypes["parsimony"].push_back(outputDir + m->getSimpleName(treefile)  +  ".parsimony");
 257
 258                         sumFile = outputDir + m->getSimpleName(treefile) + ".psummary";
 259                         m->openOutputFile(sumFile, outSum);
 260                         outputNames.push_back(sumFile);
 261                         outputTypes["psummary"].push_back(sumFile);
 262                 }else { //user wants random distribution
 263                         getUserInput();
 264
 265                         if(outputDir == "") { outputDir += m->hasPath(randomtree); }
 266                         output = new ColumnFile(outputDir+ m->getSimpleName(randomtree), itersString);
 267                         outputNames.push_back(outputDir+ m->getSimpleName(randomtree));
 268                         outputTypes["parsimony"].push_back(outputDir+ m->getSimpleName(randomtree));
 269                 }
 270
 271                 //set users groups to analyze
 272                 util = new SharedUtil();
 273                 util->setGroups(m->Groups, tmap->namesOfGroups, allGroups, numGroups, "parsimony");     //sets the groups the user wants to analyze
 274                 util->getCombos(groupComb, m->Groups, numComp);
 275                 delete util;
 276
 277                 if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
 278
 279                 pars = new Parsimony(tmap);
 280                 counter = 0;
 281
 282                 Progress* reading;
 283                 reading = new Progress("Comparing to random:", iters);
 284
 285                 if (m->control_pressed) {
 286                         delete reading; delete pars; delete output;
 287                         delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 288                         if (randomtree == "") {  outSum.close();  }
 289                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
 290                         m->Groups.clear();
 291                         return 0;
 292                 }
 293
 294
 295                 //get pscore for users tree
 296                 userData.resize(numComp,0);  //data = AB, AC, BC, ABC.
 297                 randomData.resize(numComp,0);  //data = AB, AC, BC, ABC.
 298                 rscoreFreq.resize(numComp);
 299                 uscoreFreq.resize(numComp);
 300                 rCumul.resize(numComp);
 301                 uCumul.resize(numComp);
 302                 userTreeScores.resize(numComp);
 303                 UScoreSig.resize(numComp);
 304
 305                 if (randomtree == "") {
 306                         //get pscores for users trees
 307                         for (int i = 0; i < T.size(); i++) {
 308                                 userData = pars->getValues(T[i], processors, outputDir);  //data = AB, AC, BC, ABC.
 309
 310                                 if (m->control_pressed) {
 311                                         delete reading; delete pars; delete output;
 312                                         delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 313                                         if (randomtree == "") {  outSum.close();  }
 314                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
 315                                         m->Groups.clear();
 316                                         return 0;
 317                                 }
 318
 319
 320                                 //output scores for each combination
 321                                 for(int k = 0; k < numComp; k++) {
 322
 323                                         //update uscoreFreq
 324                                         map<int,double>::iterator it = uscoreFreq[k].find(userData[k]);
 325                                         if (it == uscoreFreq[k].end()) {//new score
 326                                                 uscoreFreq[k][userData[k]] = 1;
 327                                         }else{ uscoreFreq[k][userData[k]]++; }
 328
 329                                         //add users score to valid scores
 330                                         validScores[userData[k]] = userData[k];
 331
 332                                         //save score for summary file
 333                                         userTreeScores[k].push_back(userData[k]);
 334                                 }
 335                         }
 336
 337                         //get pscores for random trees
 338                         for (int j = 0; j < iters; j++) {
 339
 340                                 //create new tree with same num nodes and leaves as users
 341                                 randT = new Tree(tmap);
 342
 343                                 //create random relationships between nodes
 344                                 randT->assembleRandomTree();
 345
 346                                 //get pscore of random tree
 347                                 randomData = pars->getValues(randT, processors, outputDir);
 348
 349                                 if (m->control_pressed) {
 350                                         delete reading; delete pars; delete output; delete randT;
 351                                         if (randomtree == "") {  outSum.close();  }
 352                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
 353                                         delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 354                                         m->Groups.clear();
 355                                         return 0;
 356                                 }
 357
 358                                 for(int r = 0; r < numComp; r++) {
 359                                         //add trees pscore to map of scores
 360                                         map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
 361                                         if (it != rscoreFreq[r].end()) {//already have that score
 362                                                 rscoreFreq[r][randomData[r]]++;
 363                                         }else{//first time we have seen this score
 364                                                 rscoreFreq[r][randomData[r]] = 1;
 365                                         }
 366
 367                                         //add randoms score to validscores
 368                                         validScores[randomData[r]] = randomData[r];
 369                                 }
 370
 371                                 //update progress bar
 372                                 reading->update(j);
 373
 374                                 delete randT;
 375                         }
 376
 377                 }else {
 378                         //get pscores for random trees
 379                         for (int j = 0; j < iters; j++) {
 380
 381                                 //create new tree with same num nodes and leaves as users
 382                                 randT = new Tree(tmap);
 383                                 //create random relationships between nodes
 384
 385                                 randT->assembleRandomTree();
 386
 387                                 if (m->control_pressed) {
 388                                         delete reading; delete pars; delete output; delete randT;
 389                                         delete tmap;
 390                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
 391                                         m->Groups.clear();
 392                                         return 0;
 393                                 }
 394
 395
 396                                 //get pscore of random tree
 397                                 randomData = pars->getValues(randT, processors, outputDir);
 398
 399                                 if (m->control_pressed) {
 400                                         delete reading; delete pars;  delete output; delete randT;
 401                                         delete tmap;
 402                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
 403                                         m->Groups.clear();
 404                                         return 0;
 405                                 }
 406
 407                                 for(int r = 0; r < numComp; r++) {
 408                                         //add trees pscore to map of scores
 409                                         map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
 410                                         if (it != rscoreFreq[r].end()) {//already have that score
 411                                                 rscoreFreq[r][randomData[r]]++;
 412                                         }else{//first time we have seen this score
 413                                                 rscoreFreq[r][randomData[r]] = 1;
 414                                         }
 415
 416                                         //add randoms score to validscores
 417                                         validScores[randomData[r]] = randomData[r];
 418                                 }
 419
 420                                 //update progress bar
 421                                 reading->update(j);
 422
 423                                 delete randT;
 424                         }
 425                 }
 426
 427                 for(int a = 0; a < numComp; a++) {
 428                         float rcumul = 0.0000;
 429                         float ucumul = 0.0000;
 430                         //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
 431                         for (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
 432                                 if (randomtree == "") {
 433                                         map<int,double>::iterator it2 = uscoreFreq[a].find(it->first);
 434                                         //user data has that score
 435                                         if (it2 != uscoreFreq[a].end()) { uscoreFreq[a][it->first] /= T.size(); ucumul+= it2->second;  }
 436                                         else { uscoreFreq[a][it->first] = 0.0000; } //no user trees with that score
 437                                         //make uCumul map
 438                                         uCumul[a][it->first] = ucumul;
 439                                 }
 440
 441                                 //make rscoreFreq map and rCumul
 442                                 map<int,double>::iterator it2 = rscoreFreq[a].find(it->first);
 443                                 //get percentage of random trees with that info
 444                                 if (it2 != rscoreFreq[a].end()) {  rscoreFreq[a][it->first] /= iters; rcumul+= it2->second;  }
 445                                 else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
 446                                 rCumul[a][it->first] = rcumul;
 447                         }
 448
 449                         //find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
 450                         for (int h = 0; h < userTreeScores[a].size(); h++) {
 451                                 UScoreSig[a].push_back(rCumul[a][userTreeScores[a][h]]);
 452                         }
 453                 }
 454
 455                 if (m->control_pressed) {
 456                                 delete reading; delete pars; delete output;
 457                                 delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 458                                 if (randomtree == "") {  outSum.close();  }
 459                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
 460                                 m->Groups.clear();
 461                                 return 0;
 462                 }
 463
 464                 //finish progress bar
 465                 reading->finish();
 466                 delete reading;
 467
 468
 469                 printParsimonyFile();
 470                 if (randomtree == "") { printUSummaryFile(); }
 471
 472                 //reset groups parameter
 473                 m->Groups.clear();
 474
 475                 delete pars; delete output;
 476                 delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 477
 478                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } outputTypes.clear(); return 0;}
 479
 480                 m->mothurOutEndLine();
 481                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 482                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 483                 m->mothurOutEndLine();
 484
 485
 486                 return 0;
 487
 488         }
 489         catch(exception& e) {
 490                 m->errorOut(e, "ParsimonyCommand", "execute");
 491                 exit(1);
 492         }
 493 }
 494
 495 /***********************************************************/
 496 void ParsimonyCommand::printParsimonyFile() {
 497         try {
 498                 vector<double> data;
 499                 vector<string> tags;
 500
 501                 if (randomtree == "") {
 502                         tags.push_back("Score"); tags.push_back("UserFreq"); tags.push_back("UserCumul"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
 503                 }else {
 504                         tags.push_back("Score"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
 505                 }
 506
 507                 for(int a = 0; a < numComp; a++) {
 508                         output->initFile(groupComb[a], tags);
 509                         //print each line
 510                         for (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
 511                                 if (randomtree == "") {
 512                                         data.push_back(it->first);  data.push_back(uscoreFreq[a][it->first]); data.push_back(uCumul[a][it->first]); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
 513                                 }else{
 514                                         data.push_back(it->first);  data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
 515                                 }
 516                                 output->output(data);
 517                                 data.clear();
 518                         }
 519                         output->resetFile();
 520                 }
 521         }
 522         catch(exception& e) {
 523                 m->errorOut(e, "ParsimonyCommand", "printParsimonyFile");
 524                 exit(1);
 525         }
 526 }
 527 /***********************************************************/
 528 int ParsimonyCommand::printUSummaryFile() {
 529         try {
 530                 //column headers
 531                 outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "ParsScore" << '\t' << "ParsSig" <<  endl;
 532                 m->mothurOut("Tree#\tGroups\tParsScore\tParsSig"); m->mothurOutEndLine();
 533
 534                 //format output
 535                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 536
 537
 538                 //print each line
 539                 for (int i = 0; i< T.size(); i++) {
 540                         for(int a = 0; a < numComp; a++) {
 541                                 if (m->control_pressed) {  outSum.close(); return 0; }
 542                                 if (UScoreSig[a][i] > (1/(float)iters)) {
 543                                         outSum << setprecision(6) << i+1 << '\t' << groupComb[a]  << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
 544                                         cout << setprecision(6) << i+1 << '\t' << groupComb[a]  << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
 545                                         m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString(UScoreSig[a][i])); m->mothurOutEndLine();
 546                                 }else {
 547                                         outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length())  << '\t' << "<" << (1/float(iters)) << endl;
 548                                         cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl;
 549                                         m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString((1/float(iters)))); m->mothurOutEndLine();
 550                                 }
 551                         }
 552                 }
 553
 554                 outSum.close();
 555                 return 0;
 556         }
 557         catch(exception& e) {
 558                 m->errorOut(e, "ParsimonyCommand", "printUSummaryFile");
 559                 exit(1);
 560         }
 561 }
 562
 563 /***********************************************************/
 564 void ParsimonyCommand::getUserInput() {
 565         try {
 566
 567                 //create treemap
 568                 tmap = new TreeMap();
 569
 570                 m->mothurOut("Please enter the number of groups you would like to analyze: ");
 571                 cin >> numGroups;
 572                 m->mothurOutJustToLog(toString(numGroups)); m->mothurOutEndLine();
 573
 574                 int num, count;
 575                 count = 1;
 576                 numEachGroup.resize(numGroups, 0);
 577
 578                 for (int i = 1; i <= numGroups; i++) {
 579                         m->mothurOut("Please enter the number of sequences in group " + toString(i) +  ": ");
 580                         cin >> num;
 581                         m->mothurOutJustToLog(toString(num)); m->mothurOutEndLine();
 582
 583                         //set tmaps seqsPerGroup
 584                         tmap->seqsPerGroup[toString(i)] = num;
 585                         tmap->namesOfGroups.push_back(toString(i));
 586
 587                         //set tmaps namesOfSeqs
 588                         for (int j = 0; j < num; j++) {
 589                                 tmap->namesOfSeqs.push_back(toString(count));
 590                                 tmap->treemap[toString(count)].groupname = toString(i);
 591                                 count++;
 592                         }
 593                 }
 594
 595                 //clears buffer so next command doesn't have error
 596                 string s;
 597                 getline(cin, s);
 598
 599                 m->Treenames = tmap->namesOfSeqs;
 600
 601         }
 602         catch(exception& e) {
 603                 m->errorOut(e, "ParsimonyCommand", "getUserInput");
 604                 exit(1);
 605         }
 606 }
 607 /*****************************************************************/
 608 int ParsimonyCommand::readNamesFile() {
 609         try {
 610                 m->names.clear();
 611                 numUniquesInName = 0;
 612
 613                 ifstream in;
 614                 m->openInputFile(namefile, in);
 615
 616                 string first, second;
 617                 map<string, string>::iterator itNames;
 618
 619                 while(!in.eof()) {
 620                         in >> first >> second; m->gobble(in);
 621
 622                         numUniquesInName++;
 623
 624                         itNames = m->names.find(first);
 625                         if (itNames == m->names.end()) {
 626                                 m->names[first] = second;
 627
 628                                 //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
 629                                 vector<string> dupNames;
 630                                 m->splitAtComma(second, dupNames);
 631
 632                                 for (int i = 0; i < dupNames.size(); i++) {
 633                                         nameMap[dupNames[i]] = dupNames[i];
 634                                         if ((groupfile == "") && (i != 0)) { tmap->addSeq(dupNames[i], "Group1"); }
 635                                 }
 636                         }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); m->names.clear(); namefile = ""; return 1; }
 637                 }
 638                 in.close();
 639
 640                 return 0;
 641         }
 642         catch(exception& e) {
 643                 m->errorOut(e, "ParsimonyCommand", "readNamesFile");
 644                 exit(1);
 645         }
 646 }
 647 /***********************************************************/
 648
 649