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