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                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  78
  79                 else {
  80                         vector<string> myArray = setParameters();
  81
  82                         OptionParser parser(option);
  83                         map<string, string> parameters = parser.getParameters();
  84                         map<string,string>::iterator it;
  85
  86                         ValidParameters validParameter;
  87
  88                         //check to make sure all parameters are valid for command
  89                         for (it = parameters.begin(); it != parameters.end(); it++) {
  90                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  91                         }
  92
  93                         //initialize outputTypes
  94                         vector<string> tempOutNames;
  95                         outputTypes["parsimony"] = tempOutNames;
  96                         outputTypes["psummary"] = tempOutNames;
  97
  98                         //if the user changes the input directory command factory will send this info to us in the output parameter
  99                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 100                         if (inputDir == "not found"){   inputDir = "";          }
 101                         else {
 102                                 string path;
 103                                 it = parameters.find("tree");
 104                                 //user has given a template file
 105                                 if(it != parameters.end()){
 106                                         path = m->hasPath(it->second);
 107                                         //if the user has not given a path then, add inputdir. else leave path alone.
 108                                         if (path == "") {       parameters["tree"] = inputDir + it->second;             }
 109                                 }
 110
 111                                 it = parameters.find("group");
 112                                 //user has given a template file
 113                                 if(it != parameters.end()){
 114                                         path = m->hasPath(it->second);
 115                                         //if the user has not given a path then, add inputdir. else leave path alone.
 116                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 117                                 }
 118
 119                                 it = parameters.find("name");
 120                                 //user has given a template file
 121                                 if(it != parameters.end()){
 122                                         path = m->hasPath(it->second);
 123                                         //if the user has not given a path then, add inputdir. else leave path alone.
 124                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 125                                 }
 126                         }
 127
 128                         m->runParse = true;
 129                         m->clearGroups();
 130                         m->clearAllGroups();
 131                         m->Treenames.clear();
 132                         m->names.clear();
 133
 134                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 135
 136                         randomtree = validParameter.validFile(parameters, "random", false);             if (randomtree == "not found") { randomtree = ""; }
 137
 138                         //are you trying to use parsimony without reading a tree or saying you want random distribution
 139                         if (randomtree == "")  {
 140                                 //check for required parameters
 141                                 treefile = validParameter.validFile(parameters, "tree", true);
 142                                 if (treefile == "not open") { abort = true; }
 143                                 else if (treefile == "not found") {                             //if there is a current design file, use it
 144                                         treefile = m->getTreeFile();
 145                                         if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
 146                                         else {  m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
 147                                 }else { m->setTreeFile(treefile); }
 148
 149                                 //check for required parameters
 150                                 groupfile = validParameter.validFile(parameters, "group", true);
 151                                 if (groupfile == "not open") { abort = true; }
 152                                 else if (groupfile == "not found") { groupfile = ""; }
 153                                 else { m->setGroupFile(groupfile); }
 154
 155                                 namefile = validParameter.validFile(parameters, "name", true);
 156                                 if (namefile == "not open") { abort = true; }
 157                                 else if (namefile == "not found") { namefile = ""; }
 158                                 else { m->setNameFile(namefile); }
 159                         }
 160
 161                         //if the user changes the output directory command factory will send this info to us in the output parameter
 162                         string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found"){  outputDir = ""; if (randomtree == "")  { outputDir += m->hasPath(treefile); } }
 163
 164                         //check for optional parameter and set defaults
 165                         // ...at some point should added some additional type checking...
 166                         groups = validParameter.validFile(parameters, "groups", false);
 167                         if (groups == "not found") { groups = ""; m->clearGroups(); }
 168                         else {
 169                                 m->splitAtDash(groups, Groups);
 170                                 m->setGroups(Groups);
 171                         }
 172
 173                         itersString = validParameter.validFile(parameters, "iters", false);                     if (itersString == "not found") { itersString = "1000"; }
 174                         m->mothurConvert(itersString, iters);
 175
 176                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 177                         m->setProcessors(temp);
 178                         m->mothurConvert(temp, processors);
 179
 180                 }
 181
 182         }
 183         catch(exception& e) {
 184                 m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand");
 185                 exit(1);
 186         }
 187 }
 188 /***********************************************************/
 189 int ParsimonyCommand::execute() {
 190         try {
 191
 192                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 193
 194
 195                 //randomtree will tell us if user had their own treefile or if they just want the random distribution
 196                 //user has entered their own tree
 197                 if (randomtree == "") {
 198
 199                         m->setTreeFile(treefile);
 200
 201                         if (groupfile != "") {
 202                                 //read in group map info.
 203                                 tmap = new TreeMap(groupfile);
 204                                 tmap->readMap();
 205                         }else{ //fake out by putting everyone in one group
 206                                 Tree* tree = new Tree(treefile); delete tree;  //extracts names from tree to make faked out groupmap
 207                                 tmap = new TreeMap();
 208
 209                                 for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
 210                         }
 211
 212                         if (namefile != "") { readNamesFile(); }
 213
 214                         read = new ReadNewickTree(treefile);
 215                         int readOk = read->read(tmap);
 216
 217                         if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete tmap; delete read; return 0; }
 218
 219                         read->AssembleTrees();
 220                         T = read->getTrees();
 221                         delete read;
 222
 223                         //make sure all files match
 224                         //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.
 225                         int numNamesInTree;
 226                         if (namefile != "")  {
 227                                 if (numUniquesInName == m->Treenames.size()) {  numNamesInTree = nameMap.size();  }
 228                                 else {   numNamesInTree = m->Treenames.size();  }
 229                         }else {  numNamesInTree = m->Treenames.size();  }
 230
 231
 232                         //output any names that are in group file but not in tree
 233                         if (numNamesInTree < tmap->getNumSeqs()) {
 234                                 for (int i = 0; i < tmap->namesOfSeqs.size(); i++) {
 235                                         //is that name in the tree?
 236                                         int count = 0;
 237                                         for (int j = 0; j < m->Treenames.size(); j++) {
 238                                                 if (tmap->namesOfSeqs[i] == m->Treenames[j]) { break; } //found it
 239                                                 count++;
 240                                         }
 241
 242                                         if (m->control_pressed) {
 243                                                 delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 244                                                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
 245                                                 m->clearGroups();
 246                                                 return 0;
 247                                         }
 248
 249                                         //then you did not find it so report it
 250                                         if (count == m->Treenames.size()) {
 251                                                 //if it is in your namefile then don't remove
 252                                                 map<string, string>::iterator it = nameMap.find(tmap->namesOfSeqs[i]);
 253
 254                                                 if (it == nameMap.end()) {
 255                                                         m->mothurOut(tmap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
 256                                                         tmap->removeSeq(tmap->namesOfSeqs[i]);
 257                                                         i--; //need this because removeSeq removes name from namesOfSeqs
 258                                                 }
 259                                         }
 260                                 }
 261                         }
 262
 263                         if(outputDir == "") { outputDir += m->hasPath(treefile); }
 264                         output = new ColumnFile(outputDir + m->getSimpleName(treefile)  +  ".parsimony", itersString);
 265                         outputNames.push_back(outputDir + m->getSimpleName(treefile)  +  ".parsimony");
 266                         outputTypes["parsimony"].push_back(outputDir + m->getSimpleName(treefile)  +  ".parsimony");
 267
 268                         sumFile = outputDir + m->getSimpleName(treefile) + ".psummary";
 269                         m->openOutputFile(sumFile, outSum);
 270                         outputNames.push_back(sumFile);
 271                         outputTypes["psummary"].push_back(sumFile);
 272                 }else { //user wants random distribution
 273                         getUserInput();
 274
 275                         if(outputDir == "") { outputDir += m->hasPath(randomtree); }
 276                         output = new ColumnFile(outputDir+ m->getSimpleName(randomtree), itersString);
 277                         outputNames.push_back(outputDir+ m->getSimpleName(randomtree));
 278                         outputTypes["parsimony"].push_back(outputDir+ m->getSimpleName(randomtree));
 279                 }
 280
 281                 //set users groups to analyze
 282                 util = new SharedUtil();
 283                 vector<string> mGroups = m->getGroups();
 284                 vector<string> tGroups = tmap->getNamesOfGroups();
 285                 util->setGroups(mGroups, tGroups, allGroups, numGroups, "parsimony");   //sets the groups the user wants to analyze
 286                 util->getCombos(groupComb, mGroups, numComp);
 287                 m->setGroups(mGroups);
 288                 delete util;
 289
 290                 if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
 291
 292                 pars = new Parsimony(tmap);
 293                 counter = 0;
 294
 295                 Progress* reading;
 296                 reading = new Progress("Comparing to random:", iters);
 297
 298                 if (m->control_pressed) {
 299                         delete reading; delete pars; delete output;
 300                         delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 301                         if (randomtree == "") {  outSum.close();  }
 302                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
 303                         m->clearGroups();
 304                         return 0;
 305                 }
 306
 307
 308                 //get pscore for users tree
 309                 userData.resize(numComp,0);  //data = AB, AC, BC, ABC.
 310                 randomData.resize(numComp,0);  //data = AB, AC, BC, ABC.
 311                 rscoreFreq.resize(numComp);
 312                 uscoreFreq.resize(numComp);
 313                 rCumul.resize(numComp);
 314                 uCumul.resize(numComp);
 315                 userTreeScores.resize(numComp);
 316                 UScoreSig.resize(numComp);
 317
 318                 if (randomtree == "") {
 319                         //get pscores for users trees
 320                         for (int i = 0; i < T.size(); i++) {
 321                                 userData = pars->getValues(T[i], processors, outputDir);  //data = AB, AC, BC, ABC.
 322
 323                                 if (m->control_pressed) {
 324                                         delete reading; delete pars; delete output;
 325                                         delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 326                                         if (randomtree == "") {  outSum.close();  }
 327                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
 328                                         m->clearGroups();
 329                                         return 0;
 330                                 }
 331
 332
 333                                 //output scores for each combination
 334                                 for(int k = 0; k < numComp; k++) {
 335
 336                                         //update uscoreFreq
 337                                         map<int,double>::iterator it = uscoreFreq[k].find(userData[k]);
 338                                         if (it == uscoreFreq[k].end()) {//new score
 339                                                 uscoreFreq[k][userData[k]] = 1;
 340                                         }else{ uscoreFreq[k][userData[k]]++; }
 341
 342                                         //add users score to valid scores
 343                                         validScores[userData[k]] = userData[k];
 344
 345                                         //save score for summary file
 346                                         userTreeScores[k].push_back(userData[k]);
 347                                 }
 348                         }
 349
 350                         //get pscores for random trees
 351                         for (int j = 0; j < iters; j++) {
 352
 353                                 //create new tree with same num nodes and leaves as users
 354                                 randT = new Tree(tmap);
 355
 356                                 //create random relationships between nodes
 357                                 randT->assembleRandomTree();
 358
 359                                 //get pscore of random tree
 360                                 randomData = pars->getValues(randT, processors, outputDir);
 361
 362                                 if (m->control_pressed) {
 363                                         delete reading; delete pars; delete output; delete randT;
 364                                         if (randomtree == "") {  outSum.close();  }
 365                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
 366                                         delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 367                                         m->clearGroups();
 368                                         return 0;
 369                                 }
 370
 371                                 for(int r = 0; r < numComp; r++) {
 372                                         //add trees pscore to map of scores
 373                                         map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
 374                                         if (it != rscoreFreq[r].end()) {//already have that score
 375                                                 rscoreFreq[r][randomData[r]]++;
 376                                         }else{//first time we have seen this score
 377                                                 rscoreFreq[r][randomData[r]] = 1;
 378                                         }
 379
 380                                         //add randoms score to validscores
 381                                         validScores[randomData[r]] = randomData[r];
 382                                 }
 383
 384                                 //update progress bar
 385                                 reading->update(j);
 386
 387                                 delete randT;
 388                         }
 389
 390                 }else {
 391                         //get pscores for random trees
 392                         for (int j = 0; j < iters; j++) {
 393
 394                                 //create new tree with same num nodes and leaves as users
 395                                 randT = new Tree(tmap);
 396                                 //create random relationships between nodes
 397
 398                                 randT->assembleRandomTree();
 399
 400                                 if (m->control_pressed) {
 401                                         delete reading; delete pars; delete output; delete randT;
 402                                         delete tmap;
 403                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
 404                                         m->clearGroups();
 405                                         return 0;
 406                                 }
 407
 408
 409                                 //get pscore of random tree
 410                                 randomData = pars->getValues(randT, processors, outputDir);
 411
 412                                 if (m->control_pressed) {
 413                                         delete reading; delete pars;  delete output; delete randT;
 414                                         delete tmap;
 415                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
 416                                         m->clearGroups();
 417                                         return 0;
 418                                 }
 419
 420                                 for(int r = 0; r < numComp; r++) {
 421                                         //add trees pscore to map of scores
 422                                         map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
 423                                         if (it != rscoreFreq[r].end()) {//already have that score
 424                                                 rscoreFreq[r][randomData[r]]++;
 425                                         }else{//first time we have seen this score
 426                                                 rscoreFreq[r][randomData[r]] = 1;
 427                                         }
 428
 429                                         //add randoms score to validscores
 430                                         validScores[randomData[r]] = randomData[r];
 431                                 }
 432
 433                                 //update progress bar
 434                                 reading->update(j);
 435
 436                                 delete randT;
 437                         }
 438                 }
 439
 440                 for(int a = 0; a < numComp; a++) {
 441                         float rcumul = 0.0000;
 442                         float ucumul = 0.0000;
 443                         //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
 444                         for (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
 445                                 if (randomtree == "") {
 446                                         map<int,double>::iterator it2 = uscoreFreq[a].find(it->first);
 447                                         //user data has that score
 448                                         if (it2 != uscoreFreq[a].end()) { uscoreFreq[a][it->first] /= T.size(); ucumul+= it2->second;  }
 449                                         else { uscoreFreq[a][it->first] = 0.0000; } //no user trees with that score
 450                                         //make uCumul map
 451                                         uCumul[a][it->first] = ucumul;
 452                                 }
 453
 454                                 //make rscoreFreq map and rCumul
 455                                 map<int,double>::iterator it2 = rscoreFreq[a].find(it->first);
 456                                 //get percentage of random trees with that info
 457                                 if (it2 != rscoreFreq[a].end()) {  rscoreFreq[a][it->first] /= iters; rcumul+= it2->second;  }
 458                                 else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
 459                                 rCumul[a][it->first] = rcumul;
 460                         }
 461
 462                         //find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
 463                         for (int h = 0; h < userTreeScores[a].size(); h++) {
 464                                 UScoreSig[a].push_back(rCumul[a][userTreeScores[a][h]]);
 465                         }
 466                 }
 467
 468                 if (m->control_pressed) {
 469                                 delete reading; delete pars; delete output;
 470                                 delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 471                                 if (randomtree == "") {  outSum.close();  }
 472                                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
 473                                 m->clearGroups();
 474                                 return 0;
 475                 }
 476
 477                 //finish progress bar
 478                 reading->finish();
 479                 delete reading;
 480
 481
 482                 printParsimonyFile();
 483                 if (randomtree == "") { printUSummaryFile(); }
 484
 485                 //reset groups parameter
 486                 m->clearGroups();
 487
 488                 delete pars; delete output;
 489                 delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 490
 491                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;}
 492
 493                 m->mothurOutEndLine();
 494                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 495                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 496                 m->mothurOutEndLine();
 497
 498
 499                 return 0;
 500
 501         }
 502         catch(exception& e) {
 503                 m->errorOut(e, "ParsimonyCommand", "execute");
 504                 exit(1);
 505         }
 506 }
 507
 508 /***********************************************************/
 509 void ParsimonyCommand::printParsimonyFile() {
 510         try {
 511                 vector<double> data;
 512                 vector<string> tags;
 513
 514                 if (randomtree == "") {
 515                         tags.push_back("Score"); tags.push_back("UserFreq"); tags.push_back("UserCumul"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
 516                 }else {
 517                         tags.push_back("Score"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
 518                 }
 519
 520                 for(int a = 0; a < numComp; a++) {
 521                         output->initFile(groupComb[a], tags);
 522                         //print each line
 523                         for (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
 524                                 if (randomtree == "") {
 525                                         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]);
 526                                 }else{
 527                                         data.push_back(it->first);  data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
 528                                 }
 529                                 output->output(data);
 530                                 data.clear();
 531                         }
 532                         output->resetFile();
 533                 }
 534         }
 535         catch(exception& e) {
 536                 m->errorOut(e, "ParsimonyCommand", "printParsimonyFile");
 537                 exit(1);
 538         }
 539 }
 540 /***********************************************************/
 541 int ParsimonyCommand::printUSummaryFile() {
 542         try {
 543                 //column headers
 544                 outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "ParsScore" << '\t' << "ParsSig" <<  endl;
 545                 m->mothurOut("Tree#\tGroups\tParsScore\tParsSig"); m->mothurOutEndLine();
 546
 547                 //format output
 548                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 549
 550
 551                 //print each line
 552                 for (int i = 0; i< T.size(); i++) {
 553                         for(int a = 0; a < numComp; a++) {
 554                                 if (m->control_pressed) {  outSum.close(); return 0; }
 555                                 if (UScoreSig[a][i] > (1/(float)iters)) {
 556                                         outSum << setprecision(6) << i+1 << '\t' << groupComb[a]  << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
 557                                         cout << setprecision(6) << i+1 << '\t' << groupComb[a]  << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
 558                                         m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString(UScoreSig[a][i])); m->mothurOutEndLine();
 559                                 }else {
 560                                         outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length())  << '\t' << "<" << (1/float(iters)) << endl;
 561                                         cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl;
 562                                         m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString((1/float(iters)))); m->mothurOutEndLine();
 563                                 }
 564                         }
 565                 }
 566
 567                 outSum.close();
 568                 return 0;
 569         }
 570         catch(exception& e) {
 571                 m->errorOut(e, "ParsimonyCommand", "printUSummaryFile");
 572                 exit(1);
 573         }
 574 }
 575
 576 /***********************************************************/
 577 void ParsimonyCommand::getUserInput() {
 578         try {
 579
 580                 //create treemap
 581                 tmap = new TreeMap();
 582
 583                 m->mothurOut("Please enter the number of groups you would like to analyze: ");
 584                 cin >> numGroups;
 585                 m->mothurOutJustToLog(toString(numGroups)); m->mothurOutEndLine();
 586
 587                 int num, count;
 588                 count = 1;
 589                 numEachGroup.resize(numGroups, 0);
 590
 591
 592                 for (int i = 1; i <= numGroups; i++) {
 593                         m->mothurOut("Please enter the number of sequences in group " + toString(i) +  ": ");
 594                         cin >> num;
 595                         m->mothurOutJustToLog(toString(num)); m->mothurOutEndLine();
 596
 597                         //set tmaps seqsPerGroup
 598                         tmap->seqsPerGroup[toString(i)] = num;
 599                         tmap->addGroup(toString(i));
 600
 601                         //set tmaps namesOfSeqs
 602                         for (int j = 0; j < num; j++) {
 603                                 tmap->namesOfSeqs.push_back(toString(count));
 604                                 tmap->treemap[toString(count)].groupname = toString(i);
 605                                 count++;
 606                         }
 607                 }
 608
 609                 //clears buffer so next command doesn't have error
 610                 string s;
 611                 getline(cin, s);
 612
 613                 m->Treenames = tmap->namesOfSeqs;
 614
 615         }
 616         catch(exception& e) {
 617                 m->errorOut(e, "ParsimonyCommand", "getUserInput");
 618                 exit(1);
 619         }
 620 }
 621 /*****************************************************************/
 622 int ParsimonyCommand::readNamesFile() {
 623         try {
 624                 m->names.clear();
 625                 numUniquesInName = 0;
 626
 627                 ifstream in;
 628                 m->openInputFile(namefile, in);
 629
 630                 string first, second;
 631                 map<string, string>::iterator itNames;
 632
 633                 while(!in.eof()) {
 634                         in >> first >> second; m->gobble(in);
 635
 636                         numUniquesInName++;
 637
 638                         itNames = m->names.find(first);
 639                         if (itNames == m->names.end()) {
 640                                 m->names[first] = second;
 641
 642                                 //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
 643                                 vector<string> dupNames;
 644                                 m->splitAtComma(second, dupNames);
 645
 646                                 for (int i = 0; i < dupNames.size(); i++) {
 647                                         nameMap[dupNames[i]] = dupNames[i];
 648                                         if ((groupfile == "") && (i != 0)) { tmap->addSeq(dupNames[i], "Group1"); }
 649                                 }
 650                         }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); m->names.clear(); namefile = ""; return 1; }
 651                 }
 652                 in.close();
 653
 654                 return 0;
 655         }
 656         catch(exception& e) {
 657                 m->errorOut(e, "ParsimonyCommand", "readNamesFile");
 658                 exit(1);
 659         }
 660 }
 661 /***********************************************************/
 662
 663