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 #include "treereader.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> ParsimonyCommand::setParameters(){
  15         try {
  16                 CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","parsimony-psummary",false,true,true); parameters.push_back(ptree);
  17         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
  18         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
  19                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
  20                 CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
  21                 CommandParameter prandom("random", "String", "", "", "", "", "","",false,false); parameters.push_back(prandom);
  22                 CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
  23                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
  24                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  25                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  26
  27                 vector<string> myArray;
  28                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  29                 return myArray;
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "ParsimonyCommand", "setParameters");
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37 string ParsimonyCommand::getHelpString(){
  38         try {
  39                 string helpString = "";
  40                 helpString += "The parsimony command parameters are tree, group, name, count, random, groups, processors and iters.  tree parameter is required unless you have valid current tree file or are using random.\n";
  41                 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";
  42                 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";
  43                 helpString += "The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters).\n";
  44                 helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
  45                 helpString += "Example parsimony(random=out, iters=500).\n";
  46                 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";
  47                 helpString += "and iters is 1000.  The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n";
  48                 helpString += "Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n";
  49                 return helpString;
  50         }
  51         catch(exception& e) {
  52                 m->errorOut(e, "ParsimonyCommand", "getHelpString");
  53                 exit(1);
  54         }
  55 }
  56 //**********************************************************************************************************************
  57 string ParsimonyCommand::getOutputPattern(string type) {
  58     try {
  59         string pattern = "";
  60
  61         if (type == "parsimony") {  pattern = "[filename],parsimony"; }
  62         else if (type == "psummary") {  pattern = "[filename],psummary"; }
  63         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  64
  65         return pattern;
  66     }
  67     catch(exception& e) {
  68         m->errorOut(e, "ParsimonyCommand", "getOutputPattern");
  69         exit(1);
  70     }
  71 }
  72 //**********************************************************************************************************************
  73 ParsimonyCommand::ParsimonyCommand(){
  74         try {
  75                 abort = true; calledHelp = true;
  76                 setParameters();
  77                 vector<string> tempOutNames;
  78                 outputTypes["parsimony"] = tempOutNames;
  79                 outputTypes["psummary"] = tempOutNames;
  80         }
  81         catch(exception& e) {
  82                 m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand");
  83                 exit(1);
  84         }
  85 }
  86 /***********************************************************/
  87 ParsimonyCommand::ParsimonyCommand(string option)  {
  88         try {
  89                 abort = false; calledHelp = false;
  90                 Groups.clear();
  91
  92                 //allow user to run help
  93                 if(option == "help") { help(); abort = true; calledHelp = true; }
  94                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  95
  96                 else {
  97                         vector<string> myArray = setParameters();
  98
  99                         OptionParser parser(option);
 100                         map<string, string> parameters = parser.getParameters();
 101                         map<string,string>::iterator it;
 102
 103                         ValidParameters validParameter;
 104
 105                         //check to make sure all parameters are valid for command
 106                         for (it = parameters.begin(); it != parameters.end(); it++) {
 107                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 108                         }
 109
 110                         //initialize outputTypes
 111                         vector<string> tempOutNames;
 112                         outputTypes["parsimony"] = tempOutNames;
 113                         outputTypes["psummary"] = tempOutNames;
 114
 115                         //if the user changes the input directory command factory will send this info to us in the output parameter
 116                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 117                         if (inputDir == "not found"){   inputDir = "";          }
 118                         else {
 119                                 string path;
 120                                 it = parameters.find("tree");
 121                                 //user has given a template file
 122                                 if(it != parameters.end()){
 123                                         path = m->hasPath(it->second);
 124                                         //if the user has not given a path then, add inputdir. else leave path alone.
 125                                         if (path == "") {       parameters["tree"] = inputDir + it->second;             }
 126                                 }
 127
 128                                 it = parameters.find("group");
 129                                 //user has given a template file
 130                                 if(it != parameters.end()){
 131                                         path = m->hasPath(it->second);
 132                                         //if the user has not given a path then, add inputdir. else leave path alone.
 133                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 134                                 }
 135
 136                                 it = parameters.find("name");
 137                                 //user has given a template file
 138                                 if(it != parameters.end()){
 139                                         path = m->hasPath(it->second);
 140                                         //if the user has not given a path then, add inputdir. else leave path alone.
 141                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 142                                 }
 143
 144                 it = parameters.find("count");
 145                                 //user has given a template file
 146                                 if(it != parameters.end()){
 147                                         path = m->hasPath(it->second);
 148                                         //if the user has not given a path then, add inputdir. else leave path alone.
 149                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 150                                 }
 151                         }
 152
 153                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 154
 155                         randomtree = validParameter.validFile(parameters, "random", false);             if (randomtree == "not found") { randomtree = ""; }
 156
 157                         //are you trying to use parsimony without reading a tree or saying you want random distribution
 158                         if (randomtree == "")  {
 159                                 //check for required parameters
 160                                 treefile = validParameter.validFile(parameters, "tree", true);
 161                                 if (treefile == "not open") { treefile = ""; abort = true; }
 162                                 else if (treefile == "not found") {                             //if there is a current design file, use it
 163                                         treefile = m->getTreeFile();
 164                                         if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
 165                                         else {  m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
 166                                 }else { m->setTreeFile(treefile); }
 167
 168                                 //check for required parameters
 169                                 groupfile = validParameter.validFile(parameters, "group", true);
 170                                 if (groupfile == "not open") { abort = true; }
 171                                 else if (groupfile == "not found") { groupfile = ""; }
 172                                 else { m->setGroupFile(groupfile); }
 173
 174                                 namefile = validParameter.validFile(parameters, "name", true);
 175                                 if (namefile == "not open") { namefile = ""; abort = true; }
 176                                 else if (namefile == "not found") { namefile = ""; }
 177                                 else { m->setNameFile(namefile); }
 178
 179                 countfile = validParameter.validFile(parameters, "count", true);
 180                 if (countfile == "not open") { countfile = ""; abort = true; }
 181                 else if (countfile == "not found") { countfile = "";  }
 182                 else { m->setCountTableFile(countfile); }
 183
 184                 if ((namefile != "") && (countfile != "")) {
 185                     m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 186                 }
 187
 188                 if ((groupfile != "") && (countfile != "")) {
 189                     m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 190                 }
 191
 192                         }
 193
 194                         //if the user changes the output directory command factory will send this info to us in the output parameter
 195                         string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found"){  outputDir = ""; if (randomtree == "")  { outputDir += m->hasPath(treefile); } }
 196
 197                         //check for optional parameter and set defaults
 198                         // ...at some point should added some additional type checking...
 199                         groups = validParameter.validFile(parameters, "groups", false);
 200                         if (groups == "not found") { groups = ""; m->clearGroups(); }
 201                         else {
 202                                 m->splitAtDash(groups, Groups);
 203                                 m->setGroups(Groups);
 204                         }
 205
 206                         itersString = validParameter.validFile(parameters, "iters", false);                     if (itersString == "not found") { itersString = "1000"; }
 207                         m->mothurConvert(itersString, iters);
 208
 209                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 210                         m->setProcessors(temp);
 211                         m->mothurConvert(temp, processors);
 212
 213                         if (countfile=="") {
 214                 if (namefile == "") {
 215                     vector<string> files; files.push_back(treefile);
 216                     parser.getNameFile(files);
 217                 }
 218             }
 219
 220                 }
 221
 222         }
 223         catch(exception& e) {
 224                 m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand");
 225                 exit(1);
 226         }
 227 }
 228 /***********************************************************/
 229 int ParsimonyCommand::execute() {
 230         try {
 231
 232                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 233
 234
 235                 //randomtree will tell us if user had their own treefile or if they just want the random distribution
 236                 //user has entered their own tree
 237                 if (randomtree == "") {
 238
 239                         m->setTreeFile(treefile);
 240
 241             TreeReader* reader;
 242             if (countfile == "") { reader = new TreeReader(treefile, groupfile, namefile); }
 243             else { reader = new TreeReader(treefile, countfile); }
 244             T = reader->getTrees();
 245             ct = T[0]->getCountTable();
 246             delete reader;
 247
 248                         if(outputDir == "") { outputDir += m->hasPath(treefile); }
 249             map<string, string> variables;
 250             variables["[filename]"] = outputDir + m->getSimpleName(treefile) +  ".";
 251
 252                         output = new ColumnFile(getOutputFileName("parsimony",variables), itersString);
 253                         outputNames.push_back(getOutputFileName("parsimony",variables));
 254                         outputTypes["parsimony"].push_back(getOutputFileName("parsimony",variables));
 255
 256                         sumFile = getOutputFileName("psummary",variables);
 257                         m->openOutputFile(sumFile, outSum);
 258                         outputNames.push_back(sumFile);
 259                         outputTypes["psummary"].push_back(sumFile);
 260                 }else { //user wants random distribution
 261                         getUserInput();
 262
 263                         if(outputDir == "") { outputDir += m->hasPath(randomtree); }
 264                         output = new ColumnFile(outputDir+ m->getSimpleName(randomtree), itersString);
 265                         outputNames.push_back(outputDir+ m->getSimpleName(randomtree));
 266                         outputTypes["parsimony"].push_back(outputDir+ m->getSimpleName(randomtree));
 267                 }
 268
 269                 //set users groups to analyze
 270                 SharedUtil util;
 271                 vector<string> mGroups = m->getGroups();
 272                 vector<string> tGroups = ct->getNamesOfGroups();
 273                 util.setGroups(mGroups, tGroups, allGroups, numGroups, "parsimony");    //sets the groups the user wants to analyze
 274                 util.getCombos(groupComb, mGroups, numComp);
 275                 m->setGroups(mGroups);
 276
 277                 if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
 278
 279                 Parsimony pars;
 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 output;
 287                         delete ct; 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++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
 290                         m->clearGroups();
 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 output;
 312                                         delete ct; 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++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
 315                                         m->clearGroups();
 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(ct);
 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 output; delete randT;
 351                                         if (randomtree == "") {  outSum.close();  }
 352                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
 353                                         delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 354                                         m->clearGroups();
 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(ct);
 383                                 //create random relationships between nodes
 384
 385                                 randT->assembleRandomTree();
 386
 387                                 if (m->control_pressed) {
 388                                         delete reading; delete output; delete randT; delete ct;
 389                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;
 390                                 }
 391
 392
 393                                 //get pscore of random tree
 394                                 randomData = pars.getValues(randT, processors, outputDir);
 395
 396                                 if (m->control_pressed) {
 397                                         delete reading; delete output; delete randT; delete ct;
 398                                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;
 399                                 }
 400
 401                                 for(int r = 0; r < numComp; r++) {
 402                                         //add trees pscore to map of scores
 403                                         map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
 404                                         if (it != rscoreFreq[r].end()) {//already have that score
 405                                                 rscoreFreq[r][randomData[r]]++;
 406                                         }else{//first time we have seen this score
 407                                                 rscoreFreq[r][randomData[r]] = 1;
 408                                         }
 409
 410                                         //add randoms score to validscores
 411                                         validScores[randomData[r]] = randomData[r];
 412                                 }
 413
 414                                 //update progress bar
 415                                 reading->update(j);
 416
 417                                 delete randT;
 418                         }
 419                 }
 420
 421                 for(int a = 0; a < numComp; a++) {
 422                         float rcumul = 0.0000;
 423                         float ucumul = 0.0000;
 424                         //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
 425                         for (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
 426                                 if (randomtree == "") {
 427                                         map<int,double>::iterator it2 = uscoreFreq[a].find(it->first);
 428                                         //user data has that score
 429                                         if (it2 != uscoreFreq[a].end()) { uscoreFreq[a][it->first] /= T.size(); ucumul+= it2->second;  }
 430                                         else { uscoreFreq[a][it->first] = 0.0000; } //no user trees with that score
 431                                         //make uCumul map
 432                                         uCumul[a][it->first] = ucumul;
 433                                 }
 434
 435                                 //make rscoreFreq map and rCumul
 436                                 map<int,double>::iterator it2 = rscoreFreq[a].find(it->first);
 437                                 //get percentage of random trees with that info
 438                                 if (it2 != rscoreFreq[a].end()) {  rscoreFreq[a][it->first] /= iters; rcumul+= it2->second;  }
 439                                 else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
 440                                 rCumul[a][it->first] = rcumul;
 441                         }
 442
 443                         //find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
 444                         for (int h = 0; h < userTreeScores[a].size(); h++) {
 445                                 UScoreSig[a].push_back(rCumul[a][userTreeScores[a][h]]);
 446                         }
 447                 }
 448
 449                 if (m->control_pressed) {
 450                                 delete reading; delete output;
 451                                 delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 452                                 if (randomtree == "") {  outSum.close();  }
 453                                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
 454                                 return 0;
 455                 }
 456
 457                 //finish progress bar
 458                 reading->finish();
 459                 delete reading;
 460
 461                 printParsimonyFile();
 462                 if (randomtree == "") { printUSummaryFile(); }
 463
 464         delete output; delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 465
 466                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;}
 467
 468                 m->mothurOutEndLine();
 469                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 470                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 471                 m->mothurOutEndLine();
 472
 473
 474                 return 0;
 475
 476         }
 477         catch(exception& e) {
 478                 m->errorOut(e, "ParsimonyCommand", "execute");
 479                 exit(1);
 480         }
 481 }
 482
 483 /***********************************************************/
 484 void ParsimonyCommand::printParsimonyFile() {
 485         try {
 486                 vector<double> data;
 487                 vector<string> tags;
 488
 489                 if (randomtree == "") {
 490                         tags.push_back("Score"); tags.push_back("UserFreq"); tags.push_back("UserCumul"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
 491                 }else {
 492                         tags.push_back("Score"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
 493                 }
 494
 495                 for(int a = 0; a < numComp; a++) {
 496                         output->initFile(groupComb[a], tags);
 497                         //print each line
 498                         for (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
 499                                 if (randomtree == "") {
 500                                         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]);
 501                                 }else{
 502                                         data.push_back(it->first);  data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
 503                                 }
 504                                 output->output(data);
 505                                 data.clear();
 506                         }
 507                         output->resetFile();
 508                 }
 509         }
 510         catch(exception& e) {
 511                 m->errorOut(e, "ParsimonyCommand", "printParsimonyFile");
 512                 exit(1);
 513         }
 514 }
 515 /***********************************************************/
 516 int ParsimonyCommand::printUSummaryFile() {
 517         try {
 518                 //column headers
 519                 outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "ParsScore" << '\t' << "ParsSig" <<  endl;
 520                 m->mothurOut("Tree#\tGroups\tParsScore\tParsSig"); m->mothurOutEndLine();
 521
 522                 //format output
 523                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 524
 525
 526                 //print each line
 527                 for (int i = 0; i< T.size(); i++) {
 528                         for(int a = 0; a < numComp; a++) {
 529                                 if (m->control_pressed) {  outSum.close(); return 0; }
 530                                 if (UScoreSig[a][i] > (1/(float)iters)) {
 531                                         outSum << setprecision(6) << i+1 << '\t' << groupComb[a]  << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
 532                                         cout << setprecision(6) << i+1 << '\t' << groupComb[a]  << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
 533                                         m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString(UScoreSig[a][i])); m->mothurOutEndLine();
 534                                 }else {
 535                                         outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length())  << '\t' << "<" << (1/float(iters)) << endl;
 536                                         cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl;
 537                                         m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString((1/float(iters)))); m->mothurOutEndLine();
 538                                 }
 539                         }
 540                 }
 541
 542                 outSum.close();
 543                 return 0;
 544         }
 545         catch(exception& e) {
 546                 m->errorOut(e, "ParsimonyCommand", "printUSummaryFile");
 547                 exit(1);
 548         }
 549 }
 550
 551 /***********************************************************/
 552 void ParsimonyCommand::getUserInput() {
 553         try {
 554
 555                 //create treemap
 556                 ct = new CountTable();
 557
 558                 m->mothurOut("Please enter the number of groups you would like to analyze: ");
 559                 cin >> numGroups;
 560                 m->mothurOutJustToLog(toString(numGroups)); m->mothurOutEndLine();
 561
 562                 int num, count;
 563                 count = 1;
 564                 numEachGroup.resize(numGroups, 0);
 565
 566         set<string> nameMap;
 567         map<string, string> groupMap;
 568         set<string> gps;
 569
 570                 for (int i = 1; i <= numGroups; i++) {
 571                         m->mothurOut("Please enter the number of sequences in group " + toString(i) +  ": ");
 572                         cin >> num;
 573                         m->mothurOutJustToLog(toString(num)); m->mothurOutEndLine();
 574
 575             gps.insert(toString(i));
 576
 577                         //set tmaps namesOfSeqs
 578                         for (int j = 0; j < num; j++) {
 579                                 groupMap[toString(count)] = toString(i);
 580                                 nameMap.insert(toString(count));
 581                                 count++;
 582                         }
 583                 }
 584                 ct->createTable(nameMap, groupMap, gps);
 585
 586                 //clears buffer so next command doesn't have error
 587                 string s;
 588                 getline(cin, s);
 589
 590                 m->Treenames = ct->getNamesOfSeqs();
 591         m->runParse = false;
 592         }
 593         catch(exception& e) {
 594                 m->errorOut(e, "ParsimonyCommand", "getUserInput");
 595                 exit(1);
 596         }
 597 }
 598 /***********************************************************/
 599
 600