globaldata.cpp

   1 #include <iostream>
   2 #include <iomanip>
   3 #include <string>
   4 #include <map>
   5 #include <sstream>
   6 #include <stdexcept>
   7
   8 using namespace std;
   9
  10 #include "globaldata.hpp"
  11 #include "sparsematrix.hpp"
  12 #include "tree.h"
  13 #include "rabundvector.hpp"
  14 #include "sabundvector.hpp"
  15 #include "listvector.hpp"
  16 #include <exception>
  17 #include <iostream>
  18
  19 /*******************************************************/
  20
  21 /******************************************************/
  22 GlobalData* GlobalData::getInstance() {
  23         if( _uniqueInstance == 0 ) {
  24                 _uniqueInstance = new GlobalData();
  25         }
  26         return _uniqueInstance;
  27 }
  28 /*******************************************************/
  29
  30 /******************************************************/
  31
  32 ListVector* GlobalData::getListVector()         {       return gListVector;             }
  33 /*******************************************************/
  34
  35 /******************************************************/
  36 void GlobalData::setListVector(ListVector* lv){
  37         try {
  38                 if(gListVector != NULL){        delete gListVector;     }
  39                 gListVector = new ListVector(*lv);
  40         }
  41         catch(exception& e) {
  42                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  43                 exit(1);
  44         }
  45         catch(...) {
  46                 cout << "An unknown error has occurred in the GlobalData class function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  47                 exit(1);
  48         }
  49 }
  50
  51 /*******************************************************/
  52
  53 /******************************************************/
  54
  55 SparseMatrix* GlobalData::getSparseMatrix()     {       return gSparseMatrix;   }
  56 /*******************************************************/
  57
  58 /******************************************************/
  59 void GlobalData::setSparseMatrix(SparseMatrix* sm){
  60         try{
  61                 if(gSparseMatrix != NULL){      delete gSparseMatrix;   }
  62                 gSparseMatrix = new SparseMatrix(*sm);
  63         }
  64         catch(exception& e) {
  65                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  66                 exit(1);
  67         }
  68         catch(...) {
  69                 cout << "An unknown error has occurred in the GlobalData class function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  70                 exit(1);
  71         }
  72
  73 }
  74 /*******************************************************/
  75
  76 /******************************************************/
  77 //This function parses through the option string of the command to remove its parameters
  78 void GlobalData::parseGlobalData(string commandString, string optionText){
  79         try {
  80                 allLines = 1;
  81                 commandName = commandString; //save command name to be used by other classes
  82
  83                 //clears out data from previous read
  84                 if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) {
  85                         clear();
  86                 }
  87
  88                 //saves help request
  89                 if (commandName =="help") {
  90                         helpRequest = optionText;
  91                 }
  92
  93                 string key, value;
  94                 //reads in parameters and values
  95                 if((optionText != "") && (commandName != "help")){
  96                         while((optionText.find_first_of(',') != -1)) {  //while there are parameters
  97                                 splitAtComma(value, optionText);
  98                                 splitAtEquals(key, value);
  99
 100                                 if (key == "phylipfile" )       { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
 101                                 if (key == "columnfile" )       { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
 102                                 if (key == "listfile" )         { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
 103                                 if (key == "rabundfile" )       { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
 104                                 if (key == "sabundfile" )       { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
 105                                 if (key == "fastafile" )        { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
 106                                 if (key == "treefile" )         { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
 107                                 if (key == "namefile" )         { namefile = value;             }
 108                                 if (key == "orderfile" )        { orderfile = value;    }
 109                                 if (key == "groupfile" )        { groupfile = value;    }
 110                                 if (key == "cutoff" )           { cutoff = value;               }
 111                                 if (key == "precision" )        { precision = value;    }
 112                                 if (key == "iters" )            { iters = value;                }
 113                                 if (key == "jumble" )           { jumble = value;               }
 114                                 if (key == "freq" )                     { freq = value;                 }
 115                                 if (key == "method" )           { method = value;               }
 116                                 if (key == "fileroot" )         { fileroot = value;             }
 117
 118                                 if (key == "single") {//stores estimators in a vector
 119                                         singleEstimators.clear(); //clears out old values
 120                                         if (value == "default") { value = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; }
 121                                         splitAtDash(value, singleEstimators);
 122                                 }
 123                                 if (key == "rarefaction") {//stores estimators in a vector
 124                                         rareEstimators.clear(); //clears out old values
 125                                         if (value == "default") { value = "rarefraction"; }
 126                                         splitAtDash(value, rareEstimators);
 127                                 }
 128                                 if (key == "shared") {//stores estimators in a vector
 129                                         sharedEstimators.clear(); //clears out old values
 130                                         if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 131                                         splitAtDash(value, sharedEstimators);
 132                                 }
 133                                 if (key == "summary") { //stores summaries to be used in a vector
 134                                         summaryEstimators.clear();
 135                                         if (value == "default") { value = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
 136                                         splitAtDash(value, summaryEstimators);
 137                                 }
 138                                 if (key == "sharedsummary") { //stores sharedSummaries to be used in a vector
 139                                         sharedSummaryEstimators.clear();
 140                                         if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 141                                         splitAtDash(value, sharedSummaryEstimators);
 142                                 }
 143                                 if (key == "sharedrarefaction") { //stores sharedrarefaction to be used in a vector
 144                                         sharedRareEstimators.clear();
 145                                         if (value == "default") { value = "sharedobserved"; }
 146                                         splitAtDash(value, sharedRareEstimators);
 147                                 }
 148                                 if (key == "line") {//stores lines to be used in a vector
 149                                         lines.clear();
 150                                         line = value;
 151                                         splitAtDash(value, lines);
 152                                         allLines = 0;
 153                                 }
 154                                 if (key == "label") {//stores lines to be used in a vector
 155                                         labels.clear();
 156                                         label = value;
 157                                         splitAtDash(value, labels);
 158                                         allLines = 0;
 159                                 }
 160                         }
 161
 162                         //saves the last parameter
 163                         value = optionText;
 164                         splitAtEquals(key, value);
 165                         if (key == "phylipfile" )       { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
 166                         if (key == "columnfile" )       { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
 167                         if (key == "listfile" )         { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
 168                         if (key == "rabundfile" )       { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
 169                         if (key == "sabundfile" )       { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
 170                         if (key == "fastafile" )        { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
 171                         if (key == "treefile" )         { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
 172                         if (key == "namefile" )         { namefile = value;             }
 173                         if (key == "orderfile" )        { orderfile = value;    }
 174                         if (key == "groupfile" )        { groupfile = value;    }
 175                         if (key == "cutoff" )           { cutoff = value;               }
 176                         if (key == "precision" )        { precision = value;    }
 177                         if (key == "iters" )            { iters = value;                }
 178                         if (key == "jumble" )           { jumble = value;               }
 179                         if (key == "freq" )                     { freq = value;                 }
 180                         if (key == "method" )           { method = value;               }
 181                         if (key == "fileroot" )         { fileroot = value;             }
 182
 183                         if (key == "single") {//stores estimators in a vector
 184                                 singleEstimators.clear(); //clears out old values
 185                                 if (value == "default") { value = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; }
 186                                 splitAtDash(value, singleEstimators);
 187                         }
 188                         if (key == "rarefaction") {//stores estimators in a vector
 189                                 rareEstimators.clear(); //clears out old values
 190                                 if (value == "default") { value = "rarefraction"; }
 191                                 splitAtDash(value, rareEstimators);
 192                         }
 193                         if (key == "shared") {//stores estimators in a vector
 194                                 sharedEstimators.clear(); //clears out old values
 195                                 if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 196                                 splitAtDash(value, sharedEstimators);
 197                         }
 198                         if (key == "summary") { //stores summaries to be used in a vector
 199                                 summaryEstimators.clear();
 200                                 if (value == "default") { value = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
 201                                 splitAtDash(value, summaryEstimators);
 202                         }
 203                         if (key == "sharedsummary") { //stores sharedSummaries to be used in a vector
 204                                 sharedSummaryEstimators.clear();
 205                                 if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 206                                 splitAtDash(value, sharedSummaryEstimators);
 207                         }
 208                         if (key == "sharedrarefaction") { //stores sharedrarefaction to be used in a vector
 209                                 sharedRareEstimators.clear();
 210                                 if (value == "default") { value = "sharedobserved"; }
 211                                 splitAtDash(value, sharedRareEstimators);
 212                         }
 213
 214                         if (key == "line") {//stores lines to be used in a vector
 215                                 lines.clear();
 216                                 line = value;
 217                                 splitAtDash(value, lines);
 218                                 allLines = 0;
 219                         }
 220                         if (key == "label") {//stores lines to be used in a vector
 221                                 labels.clear();
 222                                 label = value;
 223                                 splitAtDash(value, labels);
 224                                 allLines = 0;
 225                         }
 226                 }
 227
 228                 //set format for shared
 229                 if ((listfile != "") && (groupfile != "")) { format = "shared"; }
 230
 231                 //input defaults
 232                 if (commandName == "collect.single") {
 233                         if (singleEstimators.size() == 0) { splitAtDash(single, singleEstimators); }
 234                 }
 235                 if (commandName == "rarefaction.single") {
 236                         if (rareEstimators.size() == 0) { splitAtDash(rarefaction, rareEstimators);  }
 237                 }
 238                 if (commandName == "collect.shared") {
 239                         if (sharedEstimators.size() == 0) { splitAtDash(shared, sharedEstimators); }
 240                 }
 241                 if (commandName == "summary.single") {
 242                         if (summaryEstimators.size() == 0) { splitAtDash(summary, summaryEstimators); }
 243                 }
 244                 if (commandName == "summary.shared") {
 245                         if (sharedSummaryEstimators.size() == 0) { splitAtDash(sharedsummary, sharedSummaryEstimators); }
 246                 }
 247                 if (commandName == "rarefaction.shared") {
 248                         if (sharedRareEstimators.size() == 0) { splitAtDash(sharedrarefaction, sharedRareEstimators); }
 249                 }
 250
 251
 252                 //if you have done a read.otu with a groupfile but don't want to use it anymore because you want to do single commands
 253                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
 254                         if (listfile != "") { format = "list"; }
 255                         else if (sabundfile != "") { format = "sabund"; }
 256                         else if (rabundfile != "") { format = "rabund"; }
 257                 }
 258
 259         }
 260         catch(exception& e) {
 261                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 262                 exit(1);
 263         }
 264         catch(...) {
 265                 cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 266                 exit(1);
 267         }
 268
 269 }
 270 /*******************************************************/
 271
 272 /******************************************************/
 273 // These functions give you the option parameters of the commands
 274 string GlobalData::getPhylipFile()              {       return phylipfile;      }
 275 string GlobalData::getColumnFile()              {       return columnfile;      }
 276 string GlobalData::getListFile()                {       return listfile;        }
 277 string GlobalData::getRabundFile()              {       return rabundfile;      }
 278 string GlobalData::getSabundFile()              {       return sabundfile;      }
 279 string GlobalData::getNameFile()                {       return namefile;        }
 280 string GlobalData::getGroupFile()               {       return groupfile;       }
 281 string GlobalData::getOrderFile()               {       return orderfile;       }
 282 string GlobalData::getTreeFile()                {       return treefile;        }
 283 string GlobalData::getFastaFile()               {       return fastafile;       }
 284 string GlobalData::getCutOff()                  {       return cutoff;          }
 285 string GlobalData::getFormat()                  {       return format;          }
 286 string GlobalData::getPrecision()               {       return precision;       }
 287 string GlobalData::getMethod()                  {       return method;          }
 288 string GlobalData::getFileRoot()                {       return fileroot;        }
 289 string GlobalData::getIters()                   {       return iters;           }
 290 string GlobalData::getJumble()                  {       return jumble;          }
 291 string GlobalData::getFreq()                    {       return freq;            }
 292 void GlobalData::setListFile(string file)       {       listfile = file;        inputFileName = file;}
 293 void GlobalData::setRabundFile(string file)     {       rabundfile = file;      inputFileName = file;}
 294 void GlobalData::setSabundFile(string file)     {       sabundfile = file;      inputFileName = file;}
 295 void GlobalData::setPhylipFile(string file)     {       phylipfile = file;    inputFileName = file;}
 296 void GlobalData::setColumnFile(string file)     {       columnfile = file;    inputFileName = file;}
 297 //void GlobalData::setGroupFile(string file)    {       groupfile = file;       }
 298 void GlobalData::setNameFile(string file)       {       namefile = file;        }
 299 void GlobalData::setFormat(string Format)       {       format = Format;        }
 300
 301
 302 /*******************************************************/
 303
 304 /******************************************************/
 305
 306 GlobalData::GlobalData() {
 307         //option definitions should go here...
 308         helpRequest = "";
 309         clear();
 310 }
 311 /*******************************************************/
 312
 313 /******************************************************/
 314
 315 void GlobalData::clear() {
 316         //option definitions should go here...
 317         phylipfile              =       "";
 318         columnfile              =       "";
 319         listfile                =       "";
 320         rabundfile              =       "";
 321         sabundfile              =       "";
 322         namefile                =       "";
 323         groupfile               =       "";
 324         orderfile               =       "";
 325         fastafile               =   "";
 326         treefile                =       "";
 327         cutoff                  =       "10.00";
 328         format                  =       "";
 329         precision               =       "100";
 330         iters                   =       "1000";
 331         line                    =   "";
 332         label                   =       "";
 333         jumble                  =       "1";
 334         freq                    =       "100";
 335         method                  =       "furthest";
 336         fileroot                =       "";
 337         single                  =       "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction";
 338         rarefaction             =       "rarefaction";
 339         shared                  =       "sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
 340         sharedsummary   =   "sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
 341         summary                 =       "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson";
 342         sharedrarefaction = "sharedobserved";
 343 }
 344 /*******************************************************/
 345
 346 /******************************************************/
 347
 348 GlobalData::~GlobalData() {
 349         _uniqueInstance = 0;
 350         if(gListVector != NULL)         {       delete gListVector;             }
 351         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 352         if(gorder != NULL)                      {       delete gorder;          }
 353 }
 354 /*******************************************************/
 355
 356 /******************************************************/
 357 //This function parses the estimator options and puts them in a vector
 358 void GlobalData::splitAtDash(string& estim, vector<string>& container) {
 359         try {
 360                 string individual;
 361
 362                 while (estim.find_first_of('-') != -1) {
 363                         individual = estim.substr(0,estim.find_first_of('-'));
 364                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 365                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 366                                 container.push_back(individual);
 367                         }
 368                 }
 369                 //get last one
 370                 container.push_back(estim);
 371         }
 372         catch(exception& e) {
 373                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 374                 exit(1);
 375         }
 376         catch(...) {
 377                 cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 378                 exit(1);
 379         }
 380
 381 }
 382 /*******************************************************/
 383
 384 /******************************************************/
 385 //This function parses the label options and puts them in a set
 386 void GlobalData::splitAtDash(string& estim, set<string>& container) {
 387         try {
 388                 string individual;
 389
 390                 while (estim.find_first_of('-') != -1) {
 391                         individual = estim.substr(0,estim.find_first_of('-'));
 392                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 393                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 394                                 container.insert(individual);
 395                         }
 396                 }
 397                 //get last one
 398                 container.insert(estim);
 399         }
 400         catch(exception& e) {
 401                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 402                 exit(1);
 403         }
 404         catch(...) {
 405                 cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 406                 exit(1);
 407         }
 408
 409 }
 410 /*******************************************************/
 411
 412 /******************************************************/
 413 //This function parses the line options and puts them in a set
 414 void GlobalData::splitAtDash(string& estim, set<int>& container) {
 415         try {
 416                 string individual;
 417                 int lineNum;
 418
 419                 while (estim.find_first_of('-') != -1) {
 420                         individual = estim.substr(0,estim.find_first_of('-'));
 421                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 422                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 423                                 convert(individual, lineNum); //convert the string to int
 424                                 container.insert(lineNum);
 425                         }
 426                 }
 427                 //get last one
 428                 convert(estim, lineNum); //convert the string to int
 429                 container.insert(lineNum);
 430         }
 431         catch(exception& e) {
 432                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 433                 exit(1);
 434         }
 435         catch(...) {
 436                 cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 437                 exit(1);
 438         }
 439
 440 }
 441 /*******************************************************/
 442
 443 /******************************************************/
 444
 445 //This function splits up the various option parameters
 446 void GlobalData::splitAtComma(string& prefix, string& suffix){
 447         try {
 448                 prefix = suffix.substr(0,suffix.find_first_of(','));
 449                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
 450                         suffix = suffix.substr(suffix.find_first_of(',')+2, suffix.length());
 451                 }
 452         }
 453         catch(exception& e) {
 454                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 455                 exit(1);
 456         }
 457         catch(...) {
 458                 cout << "An unknown error has occurred in the GlobalData class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 459                 exit(1);
 460         }
 461
 462 }
 463 /*******************************************************/
 464
 465 /******************************************************/
 466 //This function separates the key value from the option value i.e. distfile = "96_..."
 467 void GlobalData::splitAtEquals(string& key, string& value){
 468         try {
 469                 if(value.find_first_of('=') != -1){
 470                         key = value.substr(0,value.find_first_of('='));
 471                         if ((value.find_first_of('=')+1) <= value.length()) {
 472                                 value = value.substr(value.find_first_of('=')+1, value.length());
 473                         }
 474                 }else{
 475                         key = value;
 476                         value = 1;
 477                 }
 478         }
 479         catch(exception& e) {
 480                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 481                 exit(1);
 482         }
 483         catch(...) {
 484                 cout << "An unknown error has occurred in the GlobalData class function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 485                 exit(1);
 486         }
 487
 488 }
 489 /*******************************************************/
 490
 491 /******************************************************/