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 == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
 101                                 if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
 102                                 if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
 103                                 if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
 104                                 if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
 105                                 if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
 106                                 if (key == "treefile" )         { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
 107                                 if (key == "name" )             { namefile = value;             }
 108                                 if (key == "order" )    { orderfile = value;    }
 109                                 if (key == "group" )    { 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                                 if (key == "randomtree" )       { randomtree = value;   }
 118                                 if (key == "groups" )           { groups = value;       }
 119
 120                                 if (key == "single") {//stores estimators in a vector
 121                                         singleEstimators.clear(); //clears out old values
 122                                         if (value == "default") { value = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; }
 123                                         splitAtDash(value, singleEstimators);
 124                                 }
 125                                 if (key == "rarefaction") {//stores estimators in a vector
 126                                         rareEstimators.clear(); //clears out old values
 127                                         if (value == "default") { value = "rarefraction"; }
 128                                         splitAtDash(value, rareEstimators);
 129                                 }
 130                                 if (key == "shared") {//stores estimators in a vector
 131                                         sharedEstimators.clear(); //clears out old values
 132                                         if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 133                                         splitAtDash(value, sharedEstimators);
 134                                 }
 135                                 if (key == "summary") { //stores summaries to be used in a vector
 136                                         summaryEstimators.clear();
 137                                         if (value == "default") { value = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
 138                                         splitAtDash(value, summaryEstimators);
 139                                 }
 140                                 if (key == "sharedsummary") { //stores sharedSummaries to be used in a vector
 141                                         sharedSummaryEstimators.clear();
 142                                         if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 143                                         splitAtDash(value, sharedSummaryEstimators);
 144                                 }
 145                                 if (key == "sharedrarefaction") { //stores sharedrarefaction to be used in a vector
 146                                         sharedRareEstimators.clear();
 147                                         if (value == "default") { value = "sharedobserved"; }
 148                                         splitAtDash(value, sharedRareEstimators);
 149                                 }
 150                                 if (key == "line") {//stores lines to be used in a set
 151                                         lines.clear();
 152                                         line = value;
 153                                         label = "";
 154                                         splitAtDash(value, lines);
 155                                         allLines = 0;
 156                                 }
 157                                 if (key == "label") {//stores lines to be used in a set
 158                                         labels.clear();
 159                                         label = value;
 160                                         line = "";
 161                                         splitAtDash(value, labels);
 162                                         allLines = 0;
 163                                 }
 164                                 if (key == "groups") {//stores lines to be used in a vector
 165                                         Groups.clear();
 166                                         groups = value;
 167                                         splitAtDash(value, Groups);
 168                                 }
 169
 170                         }
 171
 172                         //saves the last parameter
 173                         value = optionText;
 174                         splitAtEquals(key, value);
 175                         if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
 176                         if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
 177                         if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
 178                         if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
 179                         if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
 180                         if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
 181                         if (key == "treefile" )         { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
 182                         if (key == "name" )             { namefile = value;             }
 183                         if (key == "order" )    { orderfile = value;    }
 184                         if (key == "group" )    { groupfile = value;    }
 185                         if (key == "cutoff" )           { cutoff = value;               }
 186                         if (key == "precision" )        { precision = value;    }
 187                         if (key == "iters" )            { iters = value;                }
 188                         if (key == "jumble" )           { jumble = value;               }
 189                         if (key == "freq" )                     { freq = value;                 }
 190                         if (key == "method" )           { method = value;               }
 191                         if (key == "fileroot" )         { fileroot = value;             }
 192                         if (key == "randomtree" )       { randomtree = value;   }
 193
 194                         if (key == "single") {//stores estimators in a vector
 195                                 singleEstimators.clear(); //clears out old values
 196                                 if (value == "default") { value = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; }
 197                                 splitAtDash(value, singleEstimators);
 198                         }
 199                         if (key == "rarefaction") {//stores estimators in a vector
 200                                 rareEstimators.clear(); //clears out old values
 201                                 if (value == "default") { value = "rarefraction"; }
 202                                 splitAtDash(value, rareEstimators);
 203                         }
 204                         if (key == "shared") {//stores estimators in a vector
 205                                 sharedEstimators.clear(); //clears out old values
 206                                 if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 207                                 splitAtDash(value, sharedEstimators);
 208                         }
 209                         if (key == "summary") { //stores summaries to be used in a vector
 210                                 summaryEstimators.clear();
 211                                 if (value == "default") { value = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
 212                                 splitAtDash(value, summaryEstimators);
 213                         }
 214                         if (key == "sharedsummary") { //stores sharedSummaries to be used in a vector
 215                                 sharedSummaryEstimators.clear();
 216                                 if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 217                                 splitAtDash(value, sharedSummaryEstimators);
 218                         }
 219                         if (key == "sharedrarefaction") { //stores sharedrarefaction to be used in a vector
 220                                 sharedRareEstimators.clear();
 221                                 if (value == "default") { value = "sharedobserved"; }
 222                                 splitAtDash(value, sharedRareEstimators);
 223                         }
 224
 225                         if (key == "line") {//stores lines to be used in a vector
 226                                 lines.clear();
 227                                 line = value;
 228                                 label = "";
 229                                 splitAtDash(value, lines);
 230                                 allLines = 0;
 231                         }
 232                         if (key == "label") {//stores lines to be used in a vector
 233                                 labels.clear();
 234                                 label = value;
 235                                 line = "";
 236                                 splitAtDash(value, labels);
 237                                 allLines = 0;
 238                         }
 239                 }
 240
 241                 //set format for shared
 242                 if ((listfile != "") && (groupfile != "")) { format = "shared"; }
 243
 244                 //input defaults
 245                 if (commandName == "collect.single") {
 246                         if (singleEstimators.size() == 0) { splitAtDash(single, singleEstimators); }
 247                 }
 248                 if (commandName == "rarefaction.single") {
 249                         if (rareEstimators.size() == 0) { splitAtDash(rarefaction, rareEstimators);  }
 250                 }
 251                 if (commandName == "collect.shared") {
 252                         if (sharedEstimators.size() == 0) { splitAtDash(shared, sharedEstimators); }
 253                 }
 254                 if (commandName == "summary.single") {
 255                         if (summaryEstimators.size() == 0) { splitAtDash(summary, summaryEstimators); }
 256                 }
 257                 if (commandName == "summary.shared") {
 258                         if (sharedSummaryEstimators.size() == 0) { splitAtDash(sharedsummary, sharedSummaryEstimators); }
 259                 }
 260                 if (commandName == "rarefaction.shared") {
 261                         if (sharedRareEstimators.size() == 0) { splitAtDash(sharedrarefaction, sharedRareEstimators); }
 262                 }
 263
 264
 265                 //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
 266                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
 267                         if (listfile != "") { format = "list"; }
 268                         else if (sabundfile != "") { format = "sabund"; }
 269                         else if (rabundfile != "") { format = "rabund"; }
 270                 }
 271
 272         }
 273         catch(exception& e) {
 274                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 275                 exit(1);
 276         }
 277         catch(...) {
 278                 cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 279                 exit(1);
 280         }
 281
 282 }
 283 /*******************************************************/
 284
 285 /******************************************************/
 286 // These functions give you the option parameters of the commands
 287 string GlobalData::getPhylipFile()              {       return phylipfile;      }
 288 string GlobalData::getColumnFile()              {       return columnfile;      }
 289 string GlobalData::getListFile()                {       return listfile;        }
 290 string GlobalData::getRabundFile()              {       return rabundfile;      }
 291 string GlobalData::getSabundFile()              {       return sabundfile;      }
 292 string GlobalData::getNameFile()                {       return namefile;        }
 293 string GlobalData::getGroupFile()               {       return groupfile;       }
 294 string GlobalData::getOrderFile()               {       return orderfile;       }
 295 string GlobalData::getTreeFile()                {       return treefile;        }
 296 string GlobalData::getFastaFile()               {       return fastafile;       }
 297 string GlobalData::getCutOff()                  {       return cutoff;          }
 298 string GlobalData::getFormat()                  {       return format;          }
 299 string GlobalData::getPrecision()               {       return precision;       }
 300 string GlobalData::getMethod()                  {       return method;          }
 301 string GlobalData::getFileRoot()                {       return fileroot;        }
 302 string GlobalData::getIters()                   {       return iters;           }
 303 string GlobalData::getJumble()                  {       return jumble;          }
 304 string GlobalData::getFreq()                    {       return freq;            }
 305 string GlobalData::getRandomTree()              {       return randomtree;      }
 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::setPhylipFile(string file)     {       phylipfile = file;    inputFileName = file;}
 310 void GlobalData::setColumnFile(string file)     {       columnfile = file;    inputFileName = file;}
 311 //void GlobalData::setGroupFile(string file)    {       groupfile = file;               }
 312 void GlobalData::setNameFile(string file)               {       namefile = file;                }
 313 void GlobalData::setFormat(string Format)               {       format = Format;                }
 314 void GlobalData::setRandomTree(string Random)   {       randomtree = Random;    }
 315
 316
 317 /*******************************************************/
 318
 319 /******************************************************/
 320
 321 GlobalData::GlobalData() {
 322         //option definitions should go here...
 323         helpRequest = "";
 324         clear();
 325 }
 326 /*******************************************************/
 327
 328 /******************************************************/
 329
 330 void GlobalData::clear() {
 331         //option definitions should go here...
 332         phylipfile              =       "";
 333         columnfile              =       "";
 334         listfile                =       "";
 335         rabundfile              =       "";
 336         sabundfile              =       "";
 337         namefile                =       "";
 338         groupfile               =       "";
 339         orderfile               =       "";
 340         fastafile               =   "";
 341         treefile                =       "";
 342         cutoff                  =       "10.00";
 343         format                  =       "";
 344         precision               =       "100";
 345         iters                   =       "1000";
 346         line                    =   "";
 347         label                   =       "";
 348         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 349         randomtree              =       "0";  //0 means user will enter some user trees, 1 means they just want the random tree distribution.
 350         freq                    =       "100";
 351         method                  =       "furthest";
 352         fileroot                =       "";
 353         single                  =       "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction";
 354         rarefaction             =       "sobs";
 355         shared                  =       "sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
 356         sharedsummary   =   "sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
 357         summary                 =       "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson";
 358         sharedrarefaction = "sharedobserved";
 359 }
 360 /*******************************************************/
 361
 362 /******************************************************/
 363
 364 GlobalData::~GlobalData() {
 365         _uniqueInstance = 0;
 366         if(gListVector != NULL)         {       delete gListVector;             }
 367         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 368         if(gorder != NULL)                      {       delete gorder;          }
 369 }
 370 /*******************************************************/
 371
 372 /******************************************************/
 373 //This function parses the estimator options and puts them in a vector
 374 void GlobalData::splitAtDash(string& estim, vector<string>& container) {
 375         try {
 376                 string individual;
 377
 378                 while (estim.find_first_of('-') != -1) {
 379                         individual = estim.substr(0,estim.find_first_of('-'));
 380                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 381                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 382                                 container.push_back(individual);
 383                         }
 384                 }
 385                 //get last one
 386                 container.push_back(estim);
 387         }
 388         catch(exception& e) {
 389                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 390                 exit(1);
 391         }
 392         catch(...) {
 393                 cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 394                 exit(1);
 395         }
 396
 397 }
 398 /*******************************************************/
 399
 400 /******************************************************/
 401 //This function parses the label options and puts them in a set
 402 void GlobalData::splitAtDash(string& estim, set<string>& container) {
 403         try {
 404                 string individual;
 405
 406                 while (estim.find_first_of('-') != -1) {
 407                         individual = estim.substr(0,estim.find_first_of('-'));
 408                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 409                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 410                                 container.insert(individual);
 411                         }
 412                 }
 413                 //get last one
 414                 container.insert(estim);
 415         }
 416         catch(exception& e) {
 417                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 418                 exit(1);
 419         }
 420         catch(...) {
 421                 cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 422                 exit(1);
 423         }
 424
 425 }
 426 /*******************************************************/
 427
 428 /******************************************************/
 429 //This function parses the line options and puts them in a set
 430 void GlobalData::splitAtDash(string& estim, set<int>& container) {
 431         try {
 432                 string individual;
 433                 int lineNum;
 434
 435                 while (estim.find_first_of('-') != -1) {
 436                         individual = estim.substr(0,estim.find_first_of('-'));
 437                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 438                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 439                                 convert(individual, lineNum); //convert the string to int
 440                                 container.insert(lineNum);
 441                         }
 442                 }
 443                 //get last one
 444                 convert(estim, lineNum); //convert the string to int
 445                 container.insert(lineNum);
 446         }
 447         catch(exception& e) {
 448                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 449                 exit(1);
 450         }
 451         catch(...) {
 452                 cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 453                 exit(1);
 454         }
 455
 456 }
 457 /*******************************************************/
 458
 459 /******************************************************/
 460
 461 //This function splits up the various option parameters
 462 void GlobalData::splitAtComma(string& prefix, string& suffix){
 463         try {
 464                 prefix = suffix.substr(0,suffix.find_first_of(','));
 465                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
 466                         suffix = suffix.substr(suffix.find_first_of(',')+2, suffix.length());
 467                 }
 468         }
 469         catch(exception& e) {
 470                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 471                 exit(1);
 472         }
 473         catch(...) {
 474                 cout << "An unknown error has occurred in the GlobalData class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 475                 exit(1);
 476         }
 477
 478 }
 479 /*******************************************************/
 480
 481 /******************************************************/
 482 //This function separates the key value from the option value i.e. distfile = "96_..."
 483 void GlobalData::splitAtEquals(string& key, string& value){
 484         try {
 485                 if(value.find_first_of('=') != -1){
 486                         key = value.substr(0,value.find_first_of('='));
 487                         if ((value.find_first_of('=')+1) <= value.length()) {
 488                                 value = value.substr(value.find_first_of('=')+1, value.length());
 489                         }
 490                 }else{
 491                         key = value;
 492                         value = 1;
 493                 }
 494         }
 495         catch(exception& e) {
 496                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 497                 exit(1);
 498         }
 499         catch(...) {
 500                 cout << "An unknown error has occurred in the GlobalData class function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 501                 exit(1);
 502         }
 503
 504 }
 505 /*******************************************************/
 506
 507 /******************************************************/