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 "rabundvector.hpp"
  13 #include "sabundvector.hpp"
  14 #include "listvector.hpp"
  15 #include <exception>
  16 #include <iostream>
  17
  18 /*******************************************************/
  19
  20 /******************************************************/
  21 GlobalData* GlobalData::getInstance() {
  22         if( _uniqueInstance == 0 ) {
  23                 _uniqueInstance = new GlobalData();
  24         }
  25         return _uniqueInstance;
  26 }
  27 /*******************************************************/
  28
  29 /******************************************************/
  30
  31 ListVector* GlobalData::getListVector()         {       return gListVector;             }
  32 /*******************************************************/
  33
  34 /******************************************************/
  35 void GlobalData::setListVector(ListVector* lv){
  36         try {
  37                 if(gListVector != NULL){        delete gListVector;     }
  38                 gListVector = new ListVector(*lv);
  39         }
  40         catch(exception& e) {
  41                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  42                 exit(1);
  43         }
  44         catch(...) {
  45                 cout << "An unknown error has occurred in the GlobalData class function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  46                 exit(1);
  47         }
  48 }
  49
  50 /*******************************************************/
  51
  52 /******************************************************/
  53
  54 SparseMatrix* GlobalData::getSparseMatrix()     {       return gSparseMatrix;   }
  55 /*******************************************************/
  56
  57 /******************************************************/
  58 void GlobalData::setSparseMatrix(SparseMatrix* sm){
  59         try{
  60                 if(gSparseMatrix != NULL){      delete gSparseMatrix;   }
  61                 gSparseMatrix = new SparseMatrix(*sm);
  62         }
  63         catch(exception& e) {
  64                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  65                 exit(1);
  66         }
  67         catch(...) {
  68                 cout << "An unknown error has occurred in the GlobalData class function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  69                 exit(1);
  70         }
  71
  72 }
  73 /*******************************************************/
  74
  75 /******************************************************/
  76 //This function parses through the option string of the command to remove its parameters
  77 void GlobalData::parseGlobalData(string commandString, string optionText){
  78         try {
  79                 allLines = 1;
  80                 commandName = commandString; //save command name to be used by other classes
  81
  82                 //clears out data from previous read and sets format
  83                 setReadFormat(commandName);
  84
  85                 //saves help request
  86                 if (commandName =="help") {
  87                         helpRequest = optionText;
  88                 }
  89
  90                 string key, value;
  91                 //reads in parameters and values
  92                 if((optionText != "") && (commandName != "help")){
  93                         while((optionText.find_first_of(',') != -1)) {  //while there are parameters
  94                                 splitAtComma(value, optionText);
  95                                 splitAtEquals(key, value);
  96
  97                                 if (key == "distfile" )         { distfile = value; inputFileName = value; fileroot = value;}
  98                                 if (key == "listfile" )         { listfile = value; inputFileName = value; fileroot = value;}
  99                                 if (key == "rabundfile" )       { rabundfile = value; inputFileName = value; fileroot = value;}
 100                                 if (key == "sabundfile" )       { sabundfile = value; inputFileName = value; fileroot = value;}
 101                                 if (key == "namefile" )         { namefile = value; }
 102                                 if (key == "orderfile" )        { orderfile = value; }
 103                                 if (key == "groupfile" )        { groupfile = value; }
 104                                 if (key == "cutoff" )           { cutoff = value; }
 105                                 if (key == "precision" )        { precision = value; }
 106                                 if (key == "iters" )            { iters = value; }
 107                                 if (key == "jumble" )           { jumble = value; }
 108                                 if (key == "freq" )                     { freq = value; }
 109                                 if (key == "method" )           { method = value; }
 110                                 if (key == "fileroot" )         { fileroot = value; }
 111
 112                                 if (key == "single") {//stores estimators in a vector
 113                                         singleEstimators.clear(); //clears out old values
 114                                         if (value == "default") { value = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; }
 115                                         splitAtDash(value, singleEstimators);
 116                                 }
 117                                 if (key == "rarefaction") {//stores estimators in a vector
 118                                         rareEstimators.clear(); //clears out old values
 119                                         if (value == "default") { value = "rarefraction"; }
 120                                         splitAtDash(value, rareEstimators);
 121                                 }
 122                                 if (key == "shared") {//stores estimators in a vector
 123                                         sharedEstimators.clear(); //clears out old values
 124                                         if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 125                                         splitAtDash(value, sharedEstimators);
 126                                 }
 127                                 if (key == "summary") { //stores summaries to be used in a vector
 128                                         summaryEstimators.clear();
 129                                         if (value == "default") { value = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
 130                                         splitAtDash(value, summaryEstimators);
 131                                 }
 132                                 if (key == "sharedsummary") { //stores sharedSummaries to be used in a vector
 133                                         sharedSummaryEstimators.clear();
 134                                         if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 135                                         splitAtDash(value, sharedSummaryEstimators);
 136                                 }
 137                                 if (key == "sharedrarefaction") { //stores sharedrarefaction to be used in a vector
 138                                         sharedRareEstimators.clear();
 139                                         if (value == "default") { value = "sharedobserved"; }
 140                                         splitAtDash(value, sharedRareEstimators);
 141                                 }
 142                                 if (key == "line") {//stores lines to be used in a vector
 143                                         lines.clear();
 144                                         line = value;
 145                                         splitAtDash(value, lines);
 146                                         allLines = 0;
 147                                 }
 148                                 if (key == "label") {//stores lines to be used in a vector
 149                                         labels.clear();
 150                                         label = value;
 151                                         splitAtDash(value, labels);
 152                                         allLines = 0;
 153                                 }
 154                         }
 155
 156                         //saves the last parameter
 157                         value = optionText;
 158                         splitAtEquals(key, value);
 159                         if (key == "distfile" )         { distfile = value; inputFileName = value; fileroot = value; }
 160                         if (key == "listfile" )         { listfile = value; inputFileName = value; fileroot = value; }
 161                         if (key == "rabundfile" )       { rabundfile = value; inputFileName = value; fileroot = value; }
 162                         if (key == "sabundfile" )       { sabundfile = value; inputFileName = value; fileroot = value; }
 163                         if (key == "namefile" )         { namefile = value; }
 164                         if (key == "orderfile" )        { orderfile = value; }
 165                         if (key == "groupfile" )        { groupfile = value; }
 166                         if (key == "cutoff" )           { cutoff = value; }
 167                         if (key == "precision" )        { precision = value; }
 168                         if (key == "iters" )            { iters = value; }
 169                         if (key == "jumble" )           { jumble = value; }
 170                         if (key == "freq" )                     { freq = value; }
 171                         if (key == "method" )           { method = value; }
 172                         if (key == "fileroot" )         { fileroot = value; }
 173
 174                         if (key == "single") {//stores estimators in a vector
 175                                 singleEstimators.clear(); //clears out old values
 176                                 if (value == "default") { value = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; }
 177                                 splitAtDash(value, singleEstimators);
 178                         }
 179                         if (key == "rarefaction") {//stores estimators in a vector
 180                                 rareEstimators.clear(); //clears out old values
 181                                 if (value == "default") { value = "rarefraction"; }
 182                                 splitAtDash(value, rareEstimators);
 183                         }
 184                         if (key == "shared") {//stores estimators in a vector
 185                                 sharedEstimators.clear(); //clears out old values
 186                                 if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 187                                 splitAtDash(value, sharedEstimators);
 188                         }
 189                         if (key == "summary") { //stores summaries to be used in a vector
 190                                 summaryEstimators.clear();
 191                                 if (value == "default") { value = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
 192                                 splitAtDash(value, summaryEstimators);
 193                         }
 194                         if (key == "sharedsummary") { //stores sharedSummaries to be used in a vector
 195                                 sharedSummaryEstimators.clear();
 196                                 if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 197                                 splitAtDash(value, sharedSummaryEstimators);
 198                         }
 199                         if (key == "sharedrarefaction") { //stores sharedrarefaction to be used in a vector
 200                                 sharedRareEstimators.clear();
 201                                 if (value == "default") { value = "sharedobserved"; }
 202                                 splitAtDash(value, sharedRareEstimators);
 203                         }
 204
 205                         if (key == "line") {//stores lines to be used in a vector
 206                                 lines.clear();
 207                                 line = value;
 208                                 splitAtDash(value, lines);
 209                                 allLines = 0;
 210                         }
 211                         if (key == "label") {//stores lines to be used in a vector
 212                                 labels.clear();
 213                                 label = value;
 214                                 splitAtDash(value, labels);
 215                                 allLines = 0;
 216                         }
 217                 }
 218
 219
 220                 //input defaults
 221                 if (commandString == "collect.single") {
 222                         if (singleEstimators.size() == 0) { splitAtDash(single, singleEstimators); }
 223                 }
 224                 if (commandString == "rarefaction.single") {
 225                         if (rareEstimators.size() == 0) { splitAtDash(rarefaction, rareEstimators);  }
 226                 }
 227                 if (commandString == "collect.shared") {
 228                         if (sharedEstimators.size() == 0) { splitAtDash(shared, sharedEstimators); }
 229                 }
 230                 if (commandString == "summary.single") {
 231                         if (summaryEstimators.size() == 0) { splitAtDash(summary, summaryEstimators); }
 232                 }
 233                 if (commandString == "summary.shared") {
 234                         if (sharedSummaryEstimators.size() == 0) { splitAtDash(sharedsummary, sharedSummaryEstimators); }
 235                 }
 236                 if (commandString == "rarefaction.shared") {
 237                         if (sharedRareEstimators.size() == 0) { splitAtDash(sharedrarefaction, sharedRareEstimators); }
 238                 }
 239
 240
 241         }
 242         catch(exception& e) {
 243                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 244                 exit(1);
 245         }
 246         catch(...) {
 247                 cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 248                 exit(1);
 249         }
 250
 251 }
 252 /*******************************************************/
 253
 254 /******************************************************/
 255 void GlobalData::setReadFormat(string command){
 256         try {
 257                 if (command == "read.phylip") {
 258                         clear();
 259                         format = "phylip";
 260                 }else if (command == "read.column") {
 261                         clear();
 262                         format = "column";
 263                 }else if (command == "read.list") {
 264                         clear();
 265                         format = "list";
 266                 }else if (command == "read.rabund") {
 267                         clear();
 268                         format = "rabund";
 269                 }else if (command == "read.sabund") {
 270                         clear();
 271                         format = "sabund";
 272                 }else if (command == "read.shared") {
 273                         clear();
 274                         format = "shared";
 275                 }else if (command == "parselist") { format = "list"; }
 276         }
 277         catch(exception& e) {
 278                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setReadFormat. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 279                 exit(1);
 280         }
 281         catch(...) {
 282                 cout << "An unknown error has occurred in the GlobalData class function setReadFormat. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 283                 exit(1);
 284         }
 285 }
 286
 287 /*******************************************************/
 288
 289 /******************************************************/
 290 // These functions give you the option parameters of the commands
 291 string GlobalData::getDistFile()                {       return distfile;        }
 292 string GlobalData::getListFile()                {       return listfile;        }
 293 string GlobalData::getRabundFile()              {       return rabundfile;      }
 294 string GlobalData::getSabundFile()              {       return sabundfile;      }
 295 string GlobalData::getNameFile()                {       return namefile;        }
 296 string GlobalData::getGroupFile()               {       return groupfile;       }
 297 string GlobalData::getOrderFile()               {       return orderfile;       }
 298 string GlobalData::getCutOff()                  {       return cutoff;          }
 299 string GlobalData::getFormat()                  {       return format;          }
 300 string GlobalData::getPrecision()               {       return precision;       }
 301 string GlobalData::getMethod()                  {       return method;          }
 302 string GlobalData::getFileRoot()                {       return fileroot;        }
 303 string GlobalData::getIters()                   {       return iters;           }
 304 string GlobalData::getJumble()                  {       return jumble;          }
 305 string GlobalData::getFreq()                    {       return freq;            }
 306 void GlobalData::setListFile(string file)       {       listfile = file;        inputFileName = file;}
 307 void GlobalData::setRabundFile(string file)     {       rabundfile = file;      inputFileName = file;}
 308 void GlobalData::setSabundFile(string file)     {       sabundfile = file;      inputFileName = file;}
 309 void GlobalData::setDistFile(string file)       {       distfile = file;    inputFileName = file;}
 310 void GlobalData::setNameFile(string file)       {       namefile = file;        }
 311 void GlobalData::setFormat(string Format)       {       format = Format;        }
 312
 313
 314 /*******************************************************/
 315
 316 /******************************************************/
 317
 318 GlobalData::GlobalData() {
 319         //option definitions should go here...
 320         helpRequest = "";
 321         clear();
 322 }
 323 /*******************************************************/
 324
 325 /******************************************************/
 326
 327 void GlobalData::clear() {
 328         //option definitions should go here...
 329         distfile                =       "";
 330         listfile                =       "";///users/westcott/desktop/s.list
 331         rabundfile              =       "";
 332         sabundfile              =       "";
 333         namefile                =       "";
 334         groupfile               =       ""; ///users/westcott/desktop/s.names
 335         orderfile               =       "";
 336         cutoff                  =       "10.00";
 337         format                  =       "";
 338         precision               =       "100";
 339         iters                   =       "1000";
 340         line                    =   "";
 341         label                   =       "";
 342         jumble                  =       "0";
 343         freq                    =       "100";
 344         method                  =       "furthest";
 345         fileroot                =       "";
 346         single                  =       "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction";
 347         rarefaction             =       "rarefaction";
 348         shared                  =       "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
 349         sharedsummary   =   "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
 350         summary                 =       "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson";
 351         sharedrarefaction = "sharedobserved";
 352 }
 353 /*******************************************************/
 354
 355 /******************************************************/
 356
 357 GlobalData::~GlobalData() {
 358         _uniqueInstance = 0;
 359         if(gListVector != NULL)         {       delete gListVector;             }
 360         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 361         if(gorder != NULL)                      {       delete gorder;          }
 362 }
 363 /*******************************************************/
 364
 365 /******************************************************/
 366 //This function parses the estimator options and puts them in a vector
 367 void GlobalData::splitAtDash(string& estim, vector<string>& container) {
 368         try {
 369                 string individual;
 370
 371                 while (estim.find_first_of('-') != -1) {
 372                         individual = estim.substr(0,estim.find_first_of('-'));
 373                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 374                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 375                                 container.push_back(individual);
 376                         }
 377                 }
 378                 //get last one
 379                 container.push_back(estim);
 380         }
 381         catch(exception& e) {
 382                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 383                 exit(1);
 384         }
 385         catch(...) {
 386                 cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 387                 exit(1);
 388         }
 389
 390 }
 391 /*******************************************************/
 392
 393 /******************************************************/
 394 //This function parses the label options and puts them in a set
 395 void GlobalData::splitAtDash(string& estim, set<string>& container) {
 396         try {
 397                 string individual;
 398
 399                 while (estim.find_first_of('-') != -1) {
 400                         individual = estim.substr(0,estim.find_first_of('-'));
 401                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 402                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 403                                 container.insert(individual);
 404                         }
 405                 }
 406                 //get last one
 407                 container.insert(estim);
 408         }
 409         catch(exception& e) {
 410                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 411                 exit(1);
 412         }
 413         catch(...) {
 414                 cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 415                 exit(1);
 416         }
 417
 418 }
 419 /*******************************************************/
 420
 421 /******************************************************/
 422 //This function parses the line options and puts them in a set
 423 void GlobalData::splitAtDash(string& estim, set<int>& container) {
 424         try {
 425                 string individual;
 426                 int lineNum;
 427
 428                 while (estim.find_first_of('-') != -1) {
 429                         individual = estim.substr(0,estim.find_first_of('-'));
 430                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 431                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 432                                 convert(individual, lineNum); //convert the string to int
 433                                 container.insert(lineNum);
 434                         }
 435                 }
 436                 //get last one
 437                 convert(estim, lineNum); //convert the string to int
 438                 container.insert(lineNum);
 439         }
 440         catch(exception& e) {
 441                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 442                 exit(1);
 443         }
 444         catch(...) {
 445                 cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 446                 exit(1);
 447         }
 448
 449 }
 450 /*******************************************************/
 451
 452 /******************************************************/
 453
 454 //This function splits up the various option parameters
 455 void GlobalData::splitAtComma(string& prefix, string& suffix){
 456         try {
 457                 prefix = suffix.substr(0,suffix.find_first_of(','));
 458                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
 459                         suffix = suffix.substr(suffix.find_first_of(',')+2, suffix.length());
 460                 }
 461         }
 462         catch(exception& e) {
 463                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 464                 exit(1);
 465         }
 466         catch(...) {
 467                 cout << "An unknown error has occurred in the GlobalData class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 468                 exit(1);
 469         }
 470
 471 }
 472 /*******************************************************/
 473
 474 /******************************************************/
 475 //This function separates the key value from the option value i.e. distfile = "96_..."
 476 void GlobalData::splitAtEquals(string& key, string& value){
 477         try {
 478                 if(value.find_first_of('=') != -1){
 479                         key = value.substr(0,value.find_first_of('='));
 480                         if ((value.find_first_of('=')+1) <= value.length()) {
 481                                 value = value.substr(value.find_first_of('=')+1, value.length());
 482                         }
 483                 }else{
 484                         key = value;
 485                         value = 1;
 486                 }
 487         }
 488         catch(exception& e) {
 489                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 490                 exit(1);
 491         }
 492         catch(...) {
 493                 cout << "An unknown error has occurred in the GlobalData class function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 494                 exit(1);
 495         }
 496
 497 }
 498 /*******************************************************/
 499
 500 /******************************************************/