libshuffcommand.cpp

   1 /*
   2  *  libshuffcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/9/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 /* This class is designed to implement an integral form of the Cramer-von Mises statistic.
  11         you may refer to the "Integration of Microbial Ecology and Statistics: A Test To Compare Gene Libraries"
  12         paper in Applied and Environmental Microbiology, Sept. 2004, p. 5485-5492 0099-2240/04/$8.00+0
  13         DOI: 10.1128/AEM.70.9.5485-5492.2004 Copyright 2004 American Society for Microbiology for more information. */
  14
  15
  16 #include "libshuffcommand.h"
  17 #include "libshuff.h"
  18 #include "slibshuff.h"
  19 #include "dlibshuff.h"
  20
  21
  22
  23 //**********************************************************************************************************************
  24 vector<string> LibShuffCommand::setParameters(){
  25         try {
  26                 CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
  27                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
  28                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  29                 CommandParameter piters("iters", "Number", "", "10000", "", "", "",false,false); parameters.push_back(piters);
  30                 CommandParameter pstep("step", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(pstep);
  31                 CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pcutoff);
  32                 CommandParameter pform("form", "Multiple", "discrete-integral", "integral", "", "", "",false,false); parameters.push_back(pform);
  33                 CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
  34                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  35                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  36
  37                 vector<string> myArray;
  38                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  39                 return myArray;
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "LibShuffCommand", "setParameters");
  43                 exit(1);
  44         }
  45 }
  46 //**********************************************************************************************************************
  47 string LibShuffCommand::getHelpString(){
  48         try {
  49                 string helpString = "";
  50                 helpString += "The libshuff command parameters are phylip, group, sim, groups, iters, step, form and cutoff.  phylip and group parameters are required, unless you have valid current files.\n";
  51                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\n";
  52                 helpString += "The group names are separated by dashes.  The iters parameter allows you to specify how many random matrices you would like compared to your matrix.\n";
  53                 helpString += "The step parameter allows you to specify change in distance you would like between each output if you are using the discrete form.\n";
  54                 helpString += "The form parameter allows you to specify if you would like to analyze your matrix using the discrete or integral form. Your options are integral or discrete.\n";
  55                 helpString += "The libshuff command should be in the following format: libshuff(groups=yourGroups, iters=yourIters, cutOff=yourCutOff, form=yourForm, step=yourStep).\n";
  56                 helpString += "Example libshuff(groups=A-B-C, iters=500, form=discrete, step=0.01, cutOff=2.0).\n";
  57                 helpString += "The default value for groups is all the groups in your groupfile, iters is 10000, cutoff is 1.0, form is integral and step is 0.01.\n";
  58                 helpString += "The libshuff command output two files: .coverage and .slsummary their descriptions are in the manual.\n";
  59                 helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e.yourIters).\n";
  60                 return helpString;
  61         }
  62         catch(exception& e) {
  63                 m->errorOut(e, "LibShuffCommand", "getHelpString");
  64                 exit(1);
  65         }
  66 }
  67 //**********************************************************************************************************************
  68 string LibShuffCommand::getOutputFileNameTag(string type, string inputName=""){
  69         try {
  70         string outputFileName = "";
  71                 map<string, vector<string> >::iterator it;
  72
  73         //is this a type this command creates
  74         it = outputTypes.find(type);
  75         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  76         else {
  77             if (type == "coverage")             {   outputFileName =  "libshuff.coverage";       }
  78             else if (type == "libshuffsummary")      {   outputFileName =  "libshuff.summary";   }
  79             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  80         }
  81         return outputFileName;
  82         }
  83         catch(exception& e) {
  84                 m->errorOut(e, "LibShuffCommand", "getOutputFileNameTag");
  85                 exit(1);
  86         }
  87 }
  88 //**********************************************************************************************************************
  89 LibShuffCommand::LibShuffCommand(){
  90         try {
  91                 abort = true; calledHelp = true;
  92                 setParameters();
  93                 vector<string> tempOutNames;
  94                 outputTypes["coverage"] = tempOutNames;
  95                 outputTypes["libshuffsummary"] = tempOutNames;
  96         }
  97         catch(exception& e) {
  98                 m->errorOut(e, "LibShuffCommand", "LibShuffCommand");
  99                 exit(1);
 100         }
 101 }
 102
 103 //**********************************************************************************************************************
 104 LibShuffCommand::LibShuffCommand(string option)  {
 105         try {
 106                 abort = false; calledHelp = false;
 107
 108                 //allow user to run help
 109                 if(option == "help") { help(); abort = true; calledHelp = true; }
 110                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 111
 112                 else {
 113                         vector<string> myArray = setParameters();
 114
 115                         OptionParser parser(option);
 116                         map<string, string> parameters = parser.getParameters();
 117                         map<string,string>::iterator it;
 118
 119                         ValidParameters validParameter;
 120
 121                         //check to make sure all parameters are valid for command
 122                         for (it = parameters.begin(); it != parameters.end(); it++) {
 123                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 124                         }
 125
 126                         //initialize outputTypes
 127                         vector<string> tempOutNames;
 128                         outputTypes["coverage"] = tempOutNames;
 129                         outputTypes["libshuffsummary"] = tempOutNames;
 130
 131                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 132                         if (inputDir == "not found"){   inputDir = "";          }
 133                         else {
 134                                 string path;
 135                                 it = parameters.find("phylip");
 136                                 //user has given a template file
 137                                 if(it != parameters.end()){
 138                                         path = m->hasPath(it->second);
 139                                         //if the user has not given a path then, add inputdir. else leave path alone.
 140                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 141                                 }
 142
 143                                 it = parameters.find("group");
 144                                 //user has given a template file
 145                                 if(it != parameters.end()){
 146                                         path = m->hasPath(it->second);
 147                                         //if the user has not given a path then, add inputdir. else leave path alone.
 148                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 149                                 }
 150                         }
 151
 152                         //check for required parameters
 153                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 154                         if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 155                         else if (phylipfile == "not found") {
 156                                 phylipfile = m->getPhylipFile();
 157                                 if (phylipfile != "") {  m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 158                                 else {
 159                                         m->mothurOut("You must provide a phylip file."); m->mothurOutEndLine();
 160                                         abort = true;
 161                                 }
 162                         }else { m->setPhylipFile(phylipfile); }
 163
 164                         //check for required parameters
 165                         groupfile = validParameter.validFile(parameters, "group", true);
 166                         if (groupfile == "not open") { groupfile = ""; abort = true; }
 167                         else if (groupfile == "not found") {
 168                                 groupfile = m->getGroupFile();
 169                                 if (groupfile != "") {  m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 170                                 else {
 171                                         m->mothurOut("You must provide a group file."); m->mothurOutEndLine();
 172                                         abort = true;
 173                                 }
 174                         }else { m->setGroupFile(groupfile); }
 175
 176                         //if the user changes the output directory command factory will send this info to us in the output parameter
 177                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 178                                 outputDir = "";
 179                                 outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it
 180                         }
 181
 182                         //check for optional parameter and set defaults
 183                         // ...at some point should added some additional type checking...
 184                         groups = validParameter.validFile(parameters, "groups", false);
 185                         if (groups == "not found") { groups = ""; savegroups = groups; }
 186                         else {
 187                                 savegroups = groups;
 188                                 m->splitAtDash(groups, Groups);
 189                                 m->setGroups(Groups);
 190                         }
 191
 192                         string temp;
 193                         temp = validParameter.validFile(parameters, "iters", false);                            if (temp == "not found") { temp = "10000"; }
 194                         m->mothurConvert(temp, iters);
 195
 196                         temp = validParameter.validFile(parameters, "cutoff", false);                           if (temp == "not found") { temp = "1.0"; }
 197                         m->mothurConvert(temp, cutOff);
 198
 199                         temp = validParameter.validFile(parameters, "step", false);                             if (temp == "not found") { temp = "0.01"; }
 200                         m->mothurConvert(temp, step);
 201
 202                         temp = validParameter.validFile(parameters, "sim", false);                              if (temp == "not found") { temp = "F"; }
 203                         sim = m->isTrue(temp);
 204
 205                         userform = validParameter.validFile(parameters, "form", false);                 if (userform == "not found") { userform = "integral"; }
 206
 207                 }
 208
 209         }
 210         catch(exception& e) {
 211                 m->errorOut(e, "LibShuffCommand", "LibShuffCommand");
 212                 exit(1);
 213         }
 214 }
 215 //**********************************************************************************************************************
 216
 217 int LibShuffCommand::execute(){
 218         try {
 219
 220                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 221
 222                 //read files
 223                 groupMap = new GroupMap(groupfile);
 224                 int error = groupMap->readMap();
 225                 if (error == 1) { delete groupMap; return 0; }
 226
 227                 ifstream in;
 228                 m->openInputFile(phylipfile, in);
 229                 matrix = new FullMatrix(in, groupMap, sim); //reads the matrix file
 230                 in.close();
 231
 232                 if (m->control_pressed) { delete groupMap; delete matrix; return 0; }
 233
 234                 //if files don't match...
 235                 if (matrix->getNumSeqs() < groupMap->getNumSeqs()) {
 236                         m->mothurOut("Your distance file contains " + toString(matrix->getNumSeqs()) + " sequences, and your group file contains " + toString(groupMap->getNumSeqs()) + " sequences.");  m->mothurOutEndLine();
 237                         //create new group file
 238                         if(outputDir == "") { outputDir += m->hasPath(groupfile); }
 239
 240                         string newGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "editted.groups";
 241                         outputNames.push_back(newGroupFile);
 242                         ofstream outGroups;
 243                         m->openOutputFile(newGroupFile, outGroups);
 244
 245                         for (int i = 0; i < matrix->getNumSeqs(); i++) {
 246                                 if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); m->mothurRemove(newGroupFile); return 0; }
 247
 248                                 Names temp = matrix->getRowInfo(i);
 249                                 outGroups << temp.seqName << '\t' << temp.groupName << endl;
 250                         }
 251                         outGroups.close();
 252
 253                         m->mothurOut(newGroupFile + " is a new group file containing only the sequence that are in your distance file. I will read this file instead."); m->mothurOutEndLine();
 254
 255                         //read new groupfile
 256                         delete groupMap;
 257                         groupfile = newGroupFile;
 258
 259                         groupMap = new GroupMap(groupfile);
 260                         groupMap->readMap();
 261
 262                         if (m->control_pressed) { delete groupMap; delete matrix; m->mothurRemove(newGroupFile); return 0; }
 263                 }
 264
 265
 266                 setGroups();                                                            //set the groups to be analyzed and sorts them
 267
 268                 if (numGroups < 2) { m->mothurOut("[ERROR]: libshuff requires at least 2 groups, you only have " + toString(numGroups) + ", aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
 269
 270                 if (m->control_pressed) { delete groupMap; delete matrix; return 0; }
 271
 272                 /********************************************************************************************/
 273                 //this is needed because when we read the matrix we sort it into groups in alphabetical order
 274                 //the rest of the command and the classes used in this command assume specific order
 275                 /********************************************************************************************/
 276                 matrix->setGroups(groupMap->getNamesOfGroups());
 277                 vector<int> sizes;
 278                 for (int i = 0; i < (groupMap->getNamesOfGroups()).size(); i++) {   sizes.push_back(groupMap->getNumSeqs((groupMap->getNamesOfGroups())[i]));  }
 279                 matrix->setSizes(sizes);
 280
 281
 282                 if(userform == "discrete"){
 283                         form = new DLibshuff(matrix, iters, step, cutOff);
 284                 }
 285                 else{
 286                         form = new SLibshuff(matrix, iters, cutOff);
 287                 }
 288
 289                 savedDXYValues = form->evaluateAll();
 290                 savedMinValues = form->getSavedMins();
 291
 292                 if (m->control_pressed) {  delete form; m->clearGroups(); delete matrix; delete groupMap; return 0; }
 293
 294                 pValueCounts.resize(numGroups);
 295                 for(int i=0;i<numGroups;i++){
 296                         pValueCounts[i].assign(numGroups, 0);
 297                 }
 298
 299                 if (m->control_pressed) {  outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; return 0; }
 300
 301                 Progress* reading = new Progress();
 302
 303                 for(int i=0;i<numGroups-1;i++) {
 304                         for(int j=i+1;j<numGroups;j++) {
 305
 306                                 if (m->control_pressed) {  outputTypes.clear();  delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
 307
 308                                 reading->newLine(groupNames[i]+'-'+groupNames[j], iters);
 309                                 int spoti = groupMap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
 310                                 int spotj = groupMap->groupIndex[groupNames[j]];
 311
 312                                 for(int p=0;p<iters;p++) {
 313
 314                                         if (m->control_pressed) {  outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
 315
 316                                         form->randomizeGroups(spoti,spotj);
 317                                         if(form->evaluatePair(spoti,spotj) >= savedDXYValues[spoti][spotj])     {       pValueCounts[i][j]++;   }
 318                                         if(form->evaluatePair(spotj,spoti) >= savedDXYValues[spotj][spoti])     {       pValueCounts[j][i]++;   }
 319
 320                                         if (m->control_pressed) {  outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
 321
 322                                         reading->update(p);
 323                                 }
 324                                 form->resetGroup(spoti);
 325                                 form->resetGroup(spotj);
 326                         }
 327                 }
 328
 329                 if (m->control_pressed) { outputTypes.clear();  delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
 330
 331                 reading->finish();
 332                 delete reading;
 333
 334                 m->mothurOutEndLine();
 335                 printSummaryFile();
 336                 printCoverageFile();
 337
 338                 //clear out users groups
 339                 m->clearGroups();
 340                 delete form;
 341
 342                 delete matrix; delete groupMap;
 343
 344                 if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0; }
 345
 346                 m->mothurOutEndLine();
 347                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 348                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 349                 m->mothurOutEndLine();
 350
 351                 return 0;
 352         }
 353         catch(exception& e) {
 354                 m->errorOut(e, "LibShuffCommand", "execute");
 355                 exit(1);
 356         }
 357 }
 358
 359 //**********************************************************************************************************************
 360
 361 int LibShuffCommand::printCoverageFile() {
 362         try {
 363
 364                 ofstream outCov;
 365                 summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("coverage");
 366                 m->openOutputFile(summaryFile, outCov);
 367                 outputNames.push_back(summaryFile); outputTypes["coverage"].push_back(summaryFile);
 368                 outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
 369                 //cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
 370
 371                 map<double,vector<int> > allDistances;
 372                 map<double,vector<int> >::iterator it;
 373
 374                 vector<vector<int> > indices(numGroups);
 375                 int numIndices = numGroups * numGroups;
 376
 377                 int index = 0;
 378                 for(int i=0;i<numGroups;i++){
 379                         indices[i].assign(numGroups,0);
 380                         for(int j=0;j<numGroups;j++){
 381                                 indices[i][j] = index++;
 382
 383                                 int spoti = groupMap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
 384                                 int spotj = groupMap->groupIndex[groupNames[j]];
 385
 386                                 for(int k=0;k<savedMinValues[spoti][spotj].size();k++){
 387
 388                                         if(m->control_pressed)  { outCov.close(); return 0; }
 389
 390                                         if(allDistances[savedMinValues[spoti][spotj][k]].size() != 0){
 391                                                 allDistances[savedMinValues[spoti][spotj][k]][indices[i][j]]++;
 392                                         }
 393                                         else{
 394                                                 allDistances[savedMinValues[spoti][spotj][k]].assign(numIndices, 0);
 395                                                 allDistances[savedMinValues[spoti][spotj][k]][indices[i][j]] = 1;
 396                                         }
 397                                 }
 398                         }
 399                 }
 400                 it=allDistances.begin();
 401
 402                 //cout << setprecision(8);
 403
 404                 vector<int> prevRow = it->second;
 405                 it++;
 406
 407                 for(;it!=allDistances.end();it++){
 408                         for(int i=0;i<it->second.size();i++){
 409                                 it->second[i] += prevRow[i];
 410                         }
 411                         prevRow = it->second;
 412                 }
 413
 414                 vector<int> lastRow = allDistances.rbegin()->second;
 415                 outCov << setprecision(8);
 416
 417                 outCov << "dist";
 418                 for (int i = 0; i < numGroups; i++){
 419                         outCov << '\t' << groupNames[i];
 420                 }
 421                 for (int i=0;i<numGroups;i++){
 422                         for(int j=i+1;j<numGroups;j++){
 423                                 if(m->control_pressed)  { outCov.close(); return 0; }
 424                                 outCov << '\t' << groupNames[i] << '-' << groupNames[j] << '\t';
 425                                 outCov << groupNames[j] << '-' << groupNames[i];
 426                         }
 427                 }
 428                 outCov << endl;
 429
 430                 for(it=allDistances.begin();it!=allDistances.end();it++){
 431                         outCov << it->first << '\t';
 432                         for(int i=0;i<numGroups;i++){
 433                                 outCov << it->second[indices[i][i]]/(float)lastRow[indices[i][i]] << '\t';
 434                         }
 435                         for(int i=0;i<numGroups;i++){
 436                                 for(int j=i+1;j<numGroups;j++){
 437                                         if(m->control_pressed)  { outCov.close(); return 0; }
 438
 439                                         outCov << it->second[indices[i][j]]/(float)lastRow[indices[i][j]] << '\t';
 440                                         outCov << it->second[indices[j][i]]/(float)lastRow[indices[j][i]] << '\t';
 441                                 }
 442                         }
 443                         outCov << endl;
 444                 }
 445                 outCov.close();
 446
 447                 return 0;
 448         }
 449         catch(exception& e) {
 450                 m->errorOut(e, "LibShuffCommand", "printCoverageFile");
 451                 exit(1);
 452         }
 453 }
 454
 455 //**********************************************************************************************************************
 456
 457 int LibShuffCommand::printSummaryFile() {
 458         try {
 459
 460                 ofstream outSum;
 461                 summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("libshuffsummary");
 462                 m->openOutputFile(summaryFile, outSum);
 463                 outputNames.push_back(summaryFile); outputTypes["libshuffsummary"].push_back(summaryFile);
 464
 465                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 466                 cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
 467
 468                 cout << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
 469                 m->mothurOutJustToLog("Comparison\tdCXYScore\tSignificance"); m->mothurOutEndLine();
 470                 outSum << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
 471
 472                 int precision = (int)log10(iters);
 473                 for(int i=0;i<numGroups;i++){
 474                         for(int j=i+1;j<numGroups;j++){
 475                                 if(m->control_pressed)  { outSum.close(); return 0; }
 476
 477                                 int spoti = groupMap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
 478                                 int spotj = groupMap->groupIndex[groupNames[j]];
 479
 480                                 if(pValueCounts[i][j]){
 481                                         cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
 482                                         m->mothurOutJustToLog(groupNames[i]+"-"+groupNames[j] + "\t" + toString(savedDXYValues[spoti][spotj]) + "\t" + toString((pValueCounts[i][j]/(float)iters))); m->mothurOutEndLine();
 483                                         outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
 484                                 }
 485                                 else{
 486                                         cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
 487                                         m->mothurOutJustToLog(groupNames[i]+"-"+groupNames[j] + "\t" + toString(savedDXYValues[spoti][spotj]) + "\t" + toString((1/(float)iters))); m->mothurOutEndLine();
 488                                         outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
 489                                 }
 490                                 if(pValueCounts[j][i]){
 491                                         cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
 492                                         m->mothurOutJustToLog(groupNames[j]+"-"+groupNames[i] + "\t" + toString(savedDXYValues[spotj][spoti]) + "\t" + toString((pValueCounts[j][i]/(float)iters))); m->mothurOutEndLine();
 493                                         outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
 494                                 }
 495                                 else{
 496                                         cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
 497                                         m->mothurOutJustToLog(groupNames[j]+"-"+groupNames[i] + "\t" + toString(savedDXYValues[spotj][spoti]) + "\t" + toString((1/(float)iters))); m->mothurOutEndLine();
 498                                         outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
 499                                 }
 500                         }
 501                 }
 502
 503                 outSum.close();
 504                 return 0;
 505         }
 506         catch(exception& e) {
 507                 m->errorOut(e, "LibShuffCommand", "printSummaryFile");
 508                 exit(1);
 509         }
 510 }
 511
 512 //**********************************************************************************************************************
 513
 514 void LibShuffCommand::setGroups() {
 515         try {
 516                 vector<string> myGroups = m->getGroups();
 517                 //if the user has not entered specific groups to analyze then do them all
 518                 if (m->getNumGroups() == 0) {
 519                         numGroups = groupMap->getNumGroups();
 520                         for (int i=0; i < numGroups; i++) {
 521                                 myGroups.push_back((groupMap->getNamesOfGroups())[i]);
 522                         }
 523                 } else {
 524                         if (savegroups != "all") {
 525                                 //check that groups are valid
 526                                 for (int i = 0; i < myGroups.size(); i++) {
 527                                         if (groupMap->isValidGroup(myGroups[i]) != true) {
 528                                                 m->mothurOut(myGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
 529                                                 // erase the invalid group from globaldata->Groups
 530                                                 myGroups.erase(myGroups.begin()+i);
 531                                         }
 532                                 }
 533
 534                                 //if the user only entered invalid groups
 535                                 if ((myGroups.size() == 0) || (myGroups.size() == 1)) {
 536                                         numGroups = groupMap->getNumGroups();
 537                                         for (int i=0; i < numGroups; i++) {
 538                                                 myGroups.push_back((groupMap->getNamesOfGroups())[i]);
 539                                         }
 540                                         m->mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
 541                                 } else { numGroups = myGroups.size(); }
 542                         } else { //users wants all groups
 543                                 numGroups = groupMap->getNumGroups();
 544                                 myGroups.clear();
 545                                 for (int i=0; i < numGroups; i++) {
 546                                         myGroups.push_back((groupMap->getNamesOfGroups())[i]);
 547                                 }
 548                         }
 549                 }
 550
 551                 //sort so labels match
 552                 sort(myGroups.begin(), myGroups.end());
 553
 554                 //sort
 555                 //sort(groupMap->namesOfGroups.begin(), groupMap->namesOfGroups.end());
 556
 557                 for (int i = 0; i < (groupMap->getNamesOfGroups()).size(); i++) {  groupMap->groupIndex[(groupMap->getNamesOfGroups())[i]] = i;  }
 558
 559                 groupNames = myGroups;
 560                 m->setGroups(myGroups);
 561
 562         }
 563         catch(exception& e) {
 564                 m->errorOut(e, "LibShuffCommand", "setGroups");
 565                 exit(1);
 566         }
 567 }
 568
 569 /***********************************************************/