sharedcommand.cpp

   1 /*
   2  *  sharedcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "sharedcommand.h"
  11 //********************************************************************************************************************
  12 //sorts lowest to highest
  13 inline bool compareSharedRabunds(SharedRAbundVector* left, SharedRAbundVector* right){
  14         return (left->getGroup() < right->getGroup());
  15 }
  16 //**********************************************************************************************************************
  17 vector<string> SharedCommand::setParameters(){
  18         try {
  19                 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
  20                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
  21                 CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup);
  22                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  23                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  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, "SharedCommand", "setParameters");
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37 string SharedCommand::getHelpString(){
  38         try {
  39                 string helpString = "";
  40                 helpString += "The make.shared command reads a list and group file and creates a shared file, as well as a rabund file for each group.\n";
  41                 helpString += "The make.shared command parameters are list, group, ordergroup, groups and label. list and group are required unless a current file is available.\n";
  42                 helpString += "The groups parameter allows you to indicate which groups you want to include, group names should be separated by dashes. ex. groups=A-B-C. Default is all groups in your groupfile.\n";
  43                 helpString += "The label parameter allows you to indicate which labels you want to include, label names should be separated by dashes. Default is all labels in your list file.\n";
  44                 helpString += "The ordergroup parameter allows you to indicate the order of the groups in the sharedfile, by default the groups are listed alphabetically.\n";
  45                 return helpString;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "SharedCommand", "getHelpString");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53 SharedCommand::SharedCommand(){
  54         try {
  55                 abort = true; calledHelp = true;
  56                 setParameters();
  57                 //initialize outputTypes
  58                 vector<string> tempOutNames;
  59                 outputTypes["rabund"] = tempOutNames;
  60                 outputTypes["shared"] = tempOutNames;
  61                 outputTypes["group"] = tempOutNames;
  62         }
  63         catch(exception& e) {
  64                 m->errorOut(e, "SharedCommand", "SharedCommand");
  65                 exit(1);
  66         }
  67 }
  68 //**********************************************************************************************************************
  69 SharedCommand::SharedCommand(string option)  {
  70         try {
  71                 abort = false; calledHelp = false;
  72                 allLines = 1;
  73
  74                 //allow user to run help
  75                 if(option == "help") { help(); abort = true; calledHelp = true; }
  76
  77                 else {
  78
  79                          vector<string> myArray = setParameters();
  80
  81                          OptionParser parser(option);
  82                          map<string, string> parameters = parser.getParameters();
  83
  84                          ValidParameters validParameter;
  85                          map<string, string>::iterator it;
  86
  87                          //check to make sure all parameters are valid for command
  88                          for (it = parameters.begin(); it != parameters.end(); it++) {
  89                                  if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  90                          }
  91
  92                          //if the user changes the input directory command factory will send this info to us in the output parameter
  93                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  94                          if (inputDir == "not found"){  inputDir = "";          }
  95                          else {
  96                                  string path;
  97                                  it = parameters.find("list");
  98                                  //user has given a template file
  99                                  if(it != parameters.end()){
 100                                          path = m->hasPath(it->second);
 101                                          //if the user has not given a path then, add inputdir. else leave path alone.
 102                                          if (path == "") {      parameters["list"] = inputDir + it->second;             }
 103                                  }
 104
 105                                  it = parameters.find("group");
 106                                  //user has given a template file
 107                                  if(it != parameters.end()){
 108                                          path = m->hasPath(it->second);
 109                                          //if the user has not given a path then, add inputdir. else leave path alone.
 110                                          if (path == "") {      parameters["group"] = inputDir + it->second;            }
 111                                  }
 112
 113                                  it = parameters.find("ordergroup");
 114                                  //user has given a template file
 115                                  if(it != parameters.end()){
 116                                          path = m->hasPath(it->second);
 117                                          //if the user has not given a path then, add inputdir. else leave path alone.
 118                                          if (path == "") {      parameters["ordergroup"] = inputDir + it->second;               }
 119                                  }
 120                          }
 121
 122
 123                          //if the user changes the output directory command factory will send this info to us in the output parameter
 124                          outputDir = validParameter.validFile(parameters, "outputdir", false);          if (outputDir == "not found"){  outputDir = ""; }
 125
 126                          //check for required parameters
 127                          listfile = validParameter.validFile(parameters, "list", true);
 128                          if (listfile == "not open") { listfile = ""; abort = true; }
 129                          else if (listfile == "not found") {
 130                                  listfile = m->getListFile();
 131                                  if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 132                                  else {         m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
 133                          }
 134
 135                          ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
 136                          if (ordergroupfile == "not open") { abort = true; }
 137                          else if (ordergroupfile == "not found") { ordergroupfile = ""; }
 138
 139                          groupfile = validParameter.validFile(parameters, "group", true);
 140                          if (groupfile == "not open") { groupfile = ""; abort = true; }
 141                          else if (groupfile == "not found") {
 142                                  groupfile = m->getGroupFile();
 143                                  if (groupfile != "") {
 144                                          m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine();
 145                                          groupMap = new GroupMap(groupfile);
 146
 147                                          int error = groupMap->readMap();
 148                                          if (error == 1) { abort = true; }
 149                                          m->namesOfGroups = groupMap->namesOfGroups;
 150                                  }
 151                                  else {         m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
 152                          }else {
 153                                  groupMap = new GroupMap(groupfile);
 154
 155                                  int error = groupMap->readMap();
 156                                  if (error == 1) { abort = true; }
 157                                  m->namesOfGroups = groupMap->namesOfGroups;
 158                                  m->setGroupFile(groupfile);
 159                          }
 160
 161                          string groups = validParameter.validFile(parameters, "groups", false);
 162                          if (groups == "not found") { groups = ""; }
 163                          else {
 164                                  m->splitAtDash(groups, Groups);
 165                                  m->Groups = Groups;
 166                          }
 167
 168                          //check for optional parameter and set defaults
 169                          // ...at some point should added some additional type checking...
 170                          string label = validParameter.validFile(parameters, "label", false);
 171                          if (label == "not found") { label = ""; }
 172                          else {
 173                                  if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 174                                  else { allLines = 1;  }
 175                          }
 176                 }
 177
 178         }
 179         catch(exception& e) {
 180                 m->errorOut(e, "SharedCommand", "SharedCommand");
 181                 exit(1);
 182         }
 183 }
 184 //**********************************************************************************************************************
 185
 186 int SharedCommand::execute(){
 187         try {
 188
 189                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 190
 191                 //getting output filename
 192                 filename = listfile;
 193
 194                 if (outputDir == "") { outputDir += m->hasPath(filename); }
 195
 196                 filename = outputDir + m->getRootName(m->getSimpleName(filename));
 197                 filename = filename + "shared";
 198                 outputTypes["shared"].push_back(filename);
 199
 200                 m->openOutputFile(filename, out);
 201                 pickedGroups = false;
 202
 203                 //if hte user has not specified any groups then use them all
 204                 if (Groups.size() == 0) {
 205                         Groups = groupMap->namesOfGroups; m->Groups = Groups;
 206                 }else { pickedGroups = true; }
 207
 208                 //fill filehandles with neccessary ofstreams
 209                 int i;
 210                 ofstream* temp;
 211                 for (i=0; i<Groups.size(); i++) {
 212                         temp = new ofstream;
 213                         filehandles[Groups[i]] = temp;
 214                 }
 215
 216                 //set fileroot
 217                 fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
 218
 219                 //clears file before we start to write to it below
 220                 for (int i=0; i<Groups.size(); i++) {
 221                         remove((fileroot + Groups[i] + ".rabund").c_str());
 222                         outputNames.push_back((fileroot + Groups[i] + ".rabund"));
 223                         outputTypes["rabund"].push_back((fileroot + Groups[i] + ".rabund"));
 224                 }
 225
 226                 //lookup.clear();
 227                 string errorOff = "no error";
 228                 //errorOff = "";
 229
 230                 //if user provided an order file containing the order the shared file should be in read it
 231                 if (ordergroupfile != "") { readOrderFile(); }
 232
 233                 input = new InputData(listfile, "shared");
 234                 SharedList = input->getSharedListVector();
 235                 string lastLabel = SharedList->getLabel();
 236                 vector<SharedRAbundVector*> lookup;
 237
 238                 if (m->control_pressed) {
 239                         delete input; delete SharedList; delete groupMap;
 240                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
 241                         out.close(); remove(filename.c_str());
 242                         for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 243                         return 0;
 244                 }
 245
 246                 if ((m->Groups.size() == 0) && (SharedList->getNumSeqs() != groupMap->getNumSeqs())) {  //if the user has not specified any groups and their files don't match exit with error
 247                         m->mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); m->mothurOutEndLine();
 248
 249                         out.close();
 250                         remove(filename.c_str()); //remove blank shared file you made
 251
 252                         createMisMatchFile();
 253
 254                         //delete memory
 255                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 256                                 delete it3->second;
 257                         }
 258
 259                         delete input; delete SharedList; delete groupMap;
 260
 261                         return 0;
 262                 }
 263
 264                 //if user has specified groups make new groupfile for them
 265                 if (pickedGroups) { //make new group file
 266                         string groups = "";
 267                         if (m->Groups.size() < 4) {
 268                                 for (int i = 0; i < m->Groups.size(); i++) {
 269                                         groups += m->Groups[i] + ".";
 270                                 }
 271                         }else { groups = "merge"; }
 272
 273                         string newGroupFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + groups + "groups";
 274                         outputTypes["group"].push_back(newGroupFile);
 275                         outputNames.push_back(newGroupFile);
 276                         ofstream outGroups;
 277                         m->openOutputFile(newGroupFile, outGroups);
 278
 279                         vector<string> names = groupMap->getNamesSeqs();
 280                         string groupName;
 281                         for (int i = 0; i < names.size(); i++) {
 282                                 groupName = groupMap->getGroup(names[i]);
 283                                 if (isValidGroup(groupName, m->Groups)) {
 284                                         outGroups << names[i] << '\t' << groupName << endl;
 285                                 }
 286                         }
 287                         outGroups.close();
 288                 }
 289
 290                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 291                 set<string> processedLabels;
 292                 set<string> userLabels = labels;
 293
 294                 while((SharedList != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 295                         if (m->control_pressed) {
 296                                 delete input; delete SharedList; delete groupMap;
 297                                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
 298                                 out.close(); remove(filename.c_str());
 299                                 for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 300                                 return 0;
 301                         }
 302
 303                         if(allLines == 1 || labels.count(SharedList->getLabel()) == 1){
 304
 305                                         lookup = SharedList->getSharedRAbundVector();
 306
 307                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 308                                         if (pickedGroups) { //check for otus with no seqs in them
 309                                                 eliminateZeroOTUS(lookup);
 310                                         }
 311
 312                                         if (m->control_pressed) {
 313                                                 delete input; delete SharedList; delete groupMap;
 314                                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 315                                                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
 316                                                 out.close(); remove(filename.c_str());
 317                                                 for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 318                                                 return 0;
 319                                         }
 320
 321                                         printSharedData(lookup); //prints info to the .shared file
 322                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 323
 324                                         processedLabels.insert(SharedList->getLabel());
 325                                         userLabels.erase(SharedList->getLabel());
 326                         }
 327
 328                         if ((m->anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
 329                                         string saveLabel = SharedList->getLabel();
 330
 331                                         delete SharedList;
 332                                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 333
 334                                         lookup = SharedList->getSharedRAbundVector();
 335                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 336                                         if (pickedGroups) { //check for otus with no seqs in them
 337                                                 eliminateZeroOTUS(lookup);
 338                                         }
 339
 340
 341                                         if (m->control_pressed) {
 342                                                 delete input; delete SharedList; delete groupMap;
 343                                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 344                                                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
 345                                                 out.close(); remove(filename.c_str());
 346                                                 for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 347                                                 return 0;
 348                                         }
 349
 350                                         printSharedData(lookup); //prints info to the .shared file
 351                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 352
 353                                         processedLabels.insert(SharedList->getLabel());
 354                                         userLabels.erase(SharedList->getLabel());
 355
 356                                         //restore real lastlabel to save below
 357                                         SharedList->setLabel(saveLabel);
 358                         }
 359
 360
 361                         lastLabel = SharedList->getLabel();
 362
 363                         delete SharedList;
 364                         SharedList = input->getSharedListVector(); //get new list vector to process
 365                 }
 366
 367                 //output error messages about any remaining user labels
 368                 set<string>::iterator it;
 369                 bool needToRun = false;
 370                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 371                         if (processedLabels.count(lastLabel) != 1) {
 372                                 needToRun = true;
 373                         }
 374                 }
 375
 376                 //run last label if you need to
 377                 if (needToRun == true)  {
 378                         if (SharedList != NULL) {       delete SharedList;      }
 379                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 380
 381                         lookup = SharedList->getSharedRAbundVector();
 382                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 383                         if (pickedGroups) { //check for otus with no seqs in them
 384                                 eliminateZeroOTUS(lookup);
 385                         }
 386
 387                         if (m->control_pressed) {
 388                                 delete input;  delete groupMap;
 389                                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;   }
 390                                         out.close(); remove(filename.c_str());
 391                                         for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 392                                         return 0;
 393                         }
 394
 395                         printSharedData(lookup); //prints info to the .shared file
 396                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 397                         delete SharedList;
 398                 }
 399
 400                 out.close();
 401
 402                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 403                         delete it3->second;
 404                 }
 405
 406                 delete input; delete groupMap;
 407
 408                 if (m->control_pressed) {
 409                                 remove(filename.c_str());
 410                                 for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
 411                                 return 0;
 412                 }
 413
 414                 //set rabund file as new current rabundfile
 415                 string current = "";
 416                 itTypes = outputTypes.find("rabund");
 417                 if (itTypes != outputTypes.end()) {
 418                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 419                 }
 420
 421                 itTypes = outputTypes.find("shared");
 422                 if (itTypes != outputTypes.end()) {
 423                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 424                 }
 425
 426                 itTypes = outputTypes.find("group");
 427                 if (itTypes != outputTypes.end()) {
 428                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 429                 }
 430
 431                 m->mothurOutEndLine();
 432                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 433                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 434                 m->mothurOut(filename); m->mothurOutEndLine();
 435                 m->mothurOutEndLine();
 436
 437                 return 0;
 438         }
 439         catch(exception& e) {
 440                 m->errorOut(e, "SharedCommand", "execute");
 441                 exit(1);
 442         }
 443 }
 444 //**********************************************************************************************************************
 445 void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
 446         try {
 447
 448                 if (order.size() == 0) { //user has not specified an order so do aplabetically
 449                         sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
 450
 451                         m->Groups.clear();
 452
 453                         //initialize bin values
 454                         for (int i = 0; i < thislookup.size(); i++) {
 455                                 out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 456                                 thislookup[i]->print(out);
 457
 458                                 m->Groups.push_back(thislookup[i]->getGroup());
 459
 460                                 RAbundVector rav = thislookup[i]->getRAbundVector();
 461                                 m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
 462                                 rav.print(*(filehandles[thislookup[i]->getGroup()]));
 463                                 (*(filehandles[thislookup[i]->getGroup()])).close();
 464                         }
 465                 }else{
 466                         //create a map from groupName to each sharedrabund
 467                         map<string, SharedRAbundVector*> myMap;
 468                         map<string, SharedRAbundVector*>::iterator myIt;
 469
 470                         for (int i = 0; i < thislookup.size(); i++) {
 471                                 myMap[thislookup[i]->getGroup()] = thislookup[i];
 472                         }
 473
 474                         m->Groups.clear();
 475
 476                         //loop through ordered list and print the rabund
 477                         for (int i = 0; i < order.size(); i++) {
 478                                 myIt = myMap.find(order[i]);
 479
 480                                 if(myIt != myMap.end()) { //we found it
 481                                         out << (myIt->second)->getLabel() << '\t' << (myIt->second)->getGroup() << '\t';
 482                                         (myIt->second)->print(out);
 483
 484                                         m->Groups.push_back((myIt->second)->getGroup());
 485
 486                                         RAbundVector rav = (myIt->second)->getRAbundVector();
 487                                         m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
 488                                         rav.print(*(filehandles[(myIt->second)->getGroup()]));
 489                                         (*(filehandles[(myIt->second)->getGroup()])).close();
 490                                 }else{
 491                                         m->mothurOut("Can't find shared info for " + order[i] + ", skipping."); m->mothurOutEndLine();
 492                                 }
 493                         }
 494
 495                 }
 496
 497         }
 498         catch(exception& e) {
 499                 m->errorOut(e, "SharedCommand", "printSharedData");
 500                 exit(1);
 501         }
 502 }
 503 //**********************************************************************************************************************
 504 int SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
 505         try {
 506
 507                 vector<SharedRAbundVector*> newLookup;
 508                 for (int i = 0; i < thislookup.size(); i++) {
 509                         SharedRAbundVector* temp = new SharedRAbundVector();
 510                         temp->setLabel(thislookup[i]->getLabel());
 511                         temp->setGroup(thislookup[i]->getGroup());
 512                         newLookup.push_back(temp);
 513                 }
 514
 515                 //for each bin
 516                 for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
 517                         if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
 518
 519                         //look at each sharedRabund and make sure they are not all zero
 520                         bool allZero = true;
 521                         for (int j = 0; j < thislookup.size(); j++) {
 522                                 if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
 523                         }
 524
 525                         //if they are not all zero add this bin
 526                         if (!allZero) {
 527                                 for (int j = 0; j < thislookup.size(); j++) {
 528                                         newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
 529                                 }
 530                         }
 531                         //else{  cout << "bin # " << i << " is all zeros" << endl;  }
 532                 }
 533
 534                 for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
 535                 thislookup = newLookup;
 536
 537                 return 0;
 538
 539         }
 540         catch(exception& e) {
 541                 m->errorOut(e, "SharedCommand", "eliminateZeroOTUS");
 542                 exit(1);
 543         }
 544 }
 545 //**********************************************************************************************************************
 546 int SharedCommand::createMisMatchFile() {
 547         try {
 548                 ofstream outMisMatch;
 549                 string outputMisMatchName = outputDir + m->getRootName(m->getSimpleName(listfile));
 550
 551                 //you have sequences in your list file that are not in your group file
 552                 if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) {
 553                         outputMisMatchName += "missing.group";
 554                         m->mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); m->mothurOutEndLine();
 555
 556                         m->openOutputFile(outputMisMatchName, outMisMatch);
 557
 558                         map<string, string> listNames;
 559                         map<string, string>::iterator itList;
 560
 561                         //go through list and if group returns "not found" output it
 562                         for (int i = 0; i < SharedList->getNumBins(); i++) {
 563                                 if (m->control_pressed) { outMisMatch.close(); remove(outputMisMatchName.c_str()); return 0; }
 564
 565                                 string names = SharedList->get(i);
 566
 567                                 while (names.find_first_of(',') != -1) {
 568                                         string name = names.substr(0,names.find_first_of(','));
 569                                         names = names.substr(names.find_first_of(',')+1, names.length());
 570                                         string group = groupMap->getGroup(name);
 571
 572                                         if(group == "not found") {      outMisMatch << name << endl;  }
 573
 574                                         itList = listNames.find(name);
 575                                         if (itList != listNames.end()) {  m->mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 576                                         else { listNames[name] = name; }
 577                                 }
 578
 579                                 //get last name
 580                                 string group = groupMap->getGroup(names);
 581                                 if(group == "not found") {      outMisMatch << names << endl;  }
 582
 583                                 itList = listNames.find(names);
 584                                 if (itList != listNames.end()) {  m->mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 585                                 else { listNames[names] = names; }
 586
 587                         }
 588
 589                         outMisMatch.close();
 590
 591
 592                 }else {//you have sequences in your group file that are not in you list file
 593
 594                         outputMisMatchName += "missing.name";
 595                         m->mothurOut("For a list of names that are in your group file and not in your list file, please refer to " + outputMisMatchName + "."); m->mothurOutEndLine();
 596
 597                         map<string, string> namesInList;
 598                         map<string, string>::iterator itList;
 599
 600                         //go through listfile and get names
 601                         for (int i = 0; i < SharedList->getNumBins(); i++) {
 602                                 if (m->control_pressed) {  return 0; }
 603
 604
 605                                 string names = SharedList->get(i);
 606
 607                                 while (names.find_first_of(',') != -1) {
 608                                         string name = names.substr(0,names.find_first_of(','));
 609                                         names = names.substr(names.find_first_of(',')+1, names.length());
 610
 611                                         itList = namesInList.find(name);
 612                                         if (itList != namesInList.end()) {  m->mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 613
 614                                         namesInList[name] = name;
 615
 616                                 }
 617
 618                                 itList = namesInList.find(names);
 619                                 if (itList != namesInList.end()) {  m->mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 620
 621                                 //get last name
 622                                 namesInList[names] = names;
 623                         }
 624
 625                         //get names of sequences in groupfile
 626                         vector<string> seqNames = groupMap->getNamesSeqs();
 627
 628                         map<string, string>::iterator itMatch;
 629
 630                         m->openOutputFile(outputMisMatchName, outMisMatch);
 631
 632                         //loop through names in seqNames and if they aren't in namesIn list output them
 633                         for (int i = 0; i < seqNames.size(); i++) {
 634                                 if (m->control_pressed) { outMisMatch.close(); remove(outputMisMatchName.c_str()); return 0; }
 635
 636                                 itMatch = namesInList.find(seqNames[i]);
 637
 638                                 if (itMatch == namesInList.end()) {
 639
 640                                         outMisMatch << seqNames[i] << endl;
 641                                 }
 642                         }
 643                         outMisMatch.close();
 644                 }
 645
 646                 return 0;
 647         }
 648         catch(exception& e) {
 649                 m->errorOut(e, "SharedCommand", "createMisMatchFile");
 650                 exit(1);
 651         }
 652 }
 653
 654 //**********************************************************************************************************************
 655
 656 SharedCommand::~SharedCommand(){
 657         //delete list;
 658
 659
 660 }
 661 //**********************************************************************************************************************
 662 int SharedCommand::readOrderFile() {
 663         try {
 664                 //remove old names
 665                 order.clear();
 666
 667                 ifstream in;
 668                 m->openInputFile(ordergroupfile, in);
 669                 string thisGroup;
 670
 671                 while(!in.eof()){
 672                         in >> thisGroup; m->gobble(in);
 673
 674                         order.push_back(thisGroup);
 675
 676                         if (m->control_pressed) { order.clear(); break; }
 677                 }
 678                 in.close();
 679
 680                 return 0;
 681         }
 682         catch(exception& e) {
 683                 m->errorOut(e, "SharedCommand", "readOrderFile");
 684                 exit(1);
 685         }
 686 }
 687 //**********************************************************************************************************************
 688
 689 bool SharedCommand::isValidGroup(string groupname, vector<string> groups) {
 690         try {
 691                 for (int i = 0; i < groups.size(); i++) {
 692                         if (groupname == groups[i]) { return true; }
 693                 }
 694
 695                 return false;
 696         }
 697         catch(exception& e) {
 698                 m->errorOut(e, "SharedCommand", "isValidGroup");
 699                 exit(1);
 700         }
 701 }
 702 /************************************************************/
 703
 704