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 == "tree" )             { 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 labels 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 groups 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 == "tree" )             { 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                         if (key == "groups" )           { groups = value;       }
 194
 195
 196                         if (key == "single") {//stores estimators in a vector
 197                                 singleEstimators.clear(); //clears out old values
 198                                 if (value == "default") { value = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; }
 199                                 splitAtDash(value, singleEstimators);
 200                         }
 201                         if (key == "rarefaction") {//stores estimators in a vector
 202                                 rareEstimators.clear(); //clears out old values
 203                                 if (value == "default") { value = "rarefraction"; }
 204                                 splitAtDash(value, rareEstimators);
 205                         }
 206                         if (key == "shared") {//stores estimators in a vector
 207                                 sharedEstimators.clear(); //clears out old values
 208                                 if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 209                                 splitAtDash(value, sharedEstimators);
 210                         }
 211                         if (key == "summary") { //stores summaries to be used in a vector
 212                                 summaryEstimators.clear();
 213                                 if (value == "default") { value = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
 214                                 splitAtDash(value, summaryEstimators);
 215                         }
 216                         if (key == "sharedsummary") { //stores sharedSummaries to be used in a vector
 217                                 sharedSummaryEstimators.clear();
 218                                 if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 219                                 splitAtDash(value, sharedSummaryEstimators);
 220                         }
 221                         if (key == "sharedrarefaction") { //stores sharedrarefaction to be used in a vector
 222                                 sharedRareEstimators.clear();
 223                                 if (value == "default") { value = "sharedobserved"; }
 224                                 splitAtDash(value, sharedRareEstimators);
 225                         }
 226
 227                         if (key == "line") {//stores lines to be used in a vector
 228                                 lines.clear();
 229                                 line = value;
 230                                 label = "";
 231                                 splitAtDash(value, lines);
 232                                 allLines = 0;
 233                         }
 234                         if (key == "label") {//stores lines to be used in a vector
 235                                 labels.clear();
 236                                 label = value;
 237                                 line = "";
 238                                 splitAtDash(value, labels);
 239                                 allLines = 0;
 240                         }
 241                         if (key == "groups") {//stores groups to be used in a vector
 242                                         Groups.clear();
 243                                         groups = value;
 244                                         splitAtDash(value, Groups);
 245                         }
 246
 247                 }
 248
 249                 //set format for shared
 250                 if ((listfile != "") && (groupfile != "")) { format = "shared"; }
 251
 252                 //input defaults
 253                 if (commandName == "collect.single") {
 254                         if (singleEstimators.size() == 0) { splitAtDash(single, singleEstimators); }
 255                 }
 256                 if (commandName == "rarefaction.single") {
 257                         if (rareEstimators.size() == 0) { splitAtDash(rarefaction, rareEstimators);  }
 258                 }
 259                 if (commandName == "collect.shared") {
 260                         if (sharedEstimators.size() == 0) { splitAtDash(shared, sharedEstimators); }
 261                 }
 262                 if (commandName == "summary.single") {
 263                         if (summaryEstimators.size() == 0) { splitAtDash(summary, summaryEstimators); }
 264                 }
 265                 if (commandName == "summary.shared") {
 266                         if (sharedSummaryEstimators.size() == 0) { splitAtDash(sharedsummary, sharedSummaryEstimators); }
 267                 }
 268                 if (commandName == "rarefaction.shared") {
 269                         if (sharedRareEstimators.size() == 0) { splitAtDash(sharedrarefaction, sharedRareEstimators); }
 270                 }
 271
 272
 273                 //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
 274                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
 275                         if (listfile != "") { format = "list"; }
 276                         else if (sabundfile != "") { format = "sabund"; }
 277                         else if (rabundfile != "") { format = "rabund"; }
 278                 }
 279
 280         }
 281         catch(exception& e) {
 282                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 283                 exit(1);
 284         }
 285         catch(...) {
 286                 cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 287                 exit(1);
 288         }
 289
 290 }
 291 /*******************************************************/
 292
 293 /******************************************************/
 294 // These functions give you the option parameters of the commands
 295 string GlobalData::getPhylipFile()              {       return phylipfile;      }
 296 string GlobalData::getColumnFile()              {       return columnfile;      }
 297 string GlobalData::getListFile()                {       return listfile;        }
 298 string GlobalData::getRabundFile()              {       return rabundfile;      }
 299 string GlobalData::getSabundFile()              {       return sabundfile;      }
 300 string GlobalData::getNameFile()                {       return namefile;        }
 301 string GlobalData::getGroupFile()               {       return groupfile;       }
 302 string GlobalData::getOrderFile()               {       return orderfile;       }
 303 string GlobalData::getTreeFile()                {       return treefile;        }
 304 string GlobalData::getFastaFile()               {       return fastafile;       }
 305 string GlobalData::getCutOff()                  {       return cutoff;          }
 306 string GlobalData::getFormat()                  {       return format;          }
 307 string GlobalData::getPrecision()               {       return precision;       }
 308 string GlobalData::getMethod()                  {       return method;          }
 309 string GlobalData::getFileRoot()                {       return fileroot;        }
 310 string GlobalData::getIters()                   {       return iters;           }
 311 string GlobalData::getJumble()                  {       return jumble;          }
 312 string GlobalData::getFreq()                    {       return freq;            }
 313 string GlobalData::getRandomTree()              {       return randomtree;      }
 314 void GlobalData::setListFile(string file)       {       listfile = file;        inputFileName = file;}
 315 void GlobalData::setRabundFile(string file)     {       rabundfile = file;      inputFileName = file;}
 316 void GlobalData::setSabundFile(string file)     {       sabundfile = file;      inputFileName = file;}
 317 void GlobalData::setPhylipFile(string file)     {       phylipfile = file;    inputFileName = file;}
 318 void GlobalData::setColumnFile(string file)     {       columnfile = file;    inputFileName = file;}
 319 //void GlobalData::setGroupFile(string file)    {       groupfile = file;               }
 320 void GlobalData::setNameFile(string file)               {       namefile = file;                }
 321 void GlobalData::setFormat(string Format)               {       format = Format;                }
 322 void GlobalData::setRandomTree(string Random)   {       randomtree = Random;    }
 323
 324
 325 /*******************************************************/
 326
 327 /******************************************************/
 328
 329 GlobalData::GlobalData() {
 330         //option definitions should go here...
 331         helpRequest = "";
 332         clear();
 333 }
 334 /*******************************************************/
 335
 336 /******************************************************/
 337
 338 void GlobalData::clear() {
 339         //option definitions should go here...
 340         phylipfile              =       "";
 341         columnfile              =       "";
 342         listfile                =       "";
 343         rabundfile              =       "";
 344         sabundfile              =       "";
 345         namefile                =       "";
 346         groupfile               =       "";
 347         orderfile               =       "";
 348         fastafile               =   "";
 349         treefile                =       "";
 350         cutoff                  =       "10.00";
 351         format                  =       "";
 352         precision               =       "100";
 353         iters                   =       "1000";
 354         line                    =   "";
 355         label                   =       "";
 356         groups                  =       "";
 357         jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
 358         randomtree              =       "0";  //0 means user will enter some user trees, 1 means they just want the random tree distribution.
 359         freq                    =       "100";
 360         method                  =       "furthest";
 361         fileroot                =       "";
 362         single                  =       "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction";
 363         rarefaction             =       "sobs";
 364         shared                  =       "sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
 365         sharedsummary   =   "sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
 366         summary                 =       "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson";
 367         sharedrarefaction = "sharedobserved";
 368 }
 369 /*******************************************************/
 370
 371 /******************************************************/
 372
 373 GlobalData::~GlobalData() {
 374         _uniqueInstance = 0;
 375         if(gListVector != NULL)         {       delete gListVector;             }
 376         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 377         if(gorder != NULL)                      {       delete gorder;          }
 378 }
 379 /*******************************************************/
 380
 381 /******************************************************/
 382 //This function parses the estimator options and puts them in a vector
 383 void GlobalData::splitAtDash(string& estim, vector<string>& container) {
 384         try {
 385                 string individual;
 386
 387                 while (estim.find_first_of('-') != -1) {
 388                         individual = estim.substr(0,estim.find_first_of('-'));
 389                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 390                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 391                                 container.push_back(individual);
 392                         }
 393                 }
 394                 //get last one
 395                 container.push_back(estim);
 396         }
 397         catch(exception& e) {
 398                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 399                 exit(1);
 400         }
 401         catch(...) {
 402                 cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 403                 exit(1);
 404         }
 405
 406 }
 407 /*******************************************************/
 408
 409 /******************************************************/
 410 //This function parses the label options and puts them in a set
 411 void GlobalData::splitAtDash(string& estim, set<string>& container) {
 412         try {
 413                 string individual;
 414
 415                 while (estim.find_first_of('-') != -1) {
 416                         individual = estim.substr(0,estim.find_first_of('-'));
 417                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 418                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 419                                 container.insert(individual);
 420                         }
 421                 }
 422                 //get last one
 423                 container.insert(estim);
 424         }
 425         catch(exception& e) {
 426                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 427                 exit(1);
 428         }
 429         catch(...) {
 430                 cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 431                 exit(1);
 432         }
 433
 434 }
 435 /*******************************************************/
 436
 437 /******************************************************/
 438 //This function parses the line options and puts them in a set
 439 void GlobalData::splitAtDash(string& estim, set<int>& container) {
 440         try {
 441                 string individual;
 442                 int lineNum;
 443
 444                 while (estim.find_first_of('-') != -1) {
 445                         individual = estim.substr(0,estim.find_first_of('-'));
 446                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 447                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 448                                 convert(individual, lineNum); //convert the string to int
 449                                 container.insert(lineNum);
 450                         }
 451                 }
 452                 //get last one
 453                 convert(estim, lineNum); //convert the string to int
 454                 container.insert(lineNum);
 455         }
 456         catch(exception& e) {
 457                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 458                 exit(1);
 459         }
 460         catch(...) {
 461                 cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 462                 exit(1);
 463         }
 464
 465 }
 466 /*******************************************************/
 467
 468 /******************************************************/
 469
 470 //This function splits up the various option parameters
 471 void GlobalData::splitAtComma(string& prefix, string& suffix){
 472         try {
 473                 prefix = suffix.substr(0,suffix.find_first_of(','));
 474                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
 475                         suffix = suffix.substr(suffix.find_first_of(',')+2, suffix.length());
 476                 }
 477         }
 478         catch(exception& e) {
 479                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 480                 exit(1);
 481         }
 482         catch(...) {
 483                 cout << "An unknown error has occurred in the GlobalData class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 484                 exit(1);
 485         }
 486
 487 }
 488 /*******************************************************/
 489
 490 /******************************************************/
 491 //This function separates the key value from the option value i.e. dist=96_...
 492 void GlobalData::splitAtEquals(string& key, string& value){
 493         try {
 494                 if(value.find_first_of('=') != -1){
 495                         key = value.substr(0,value.find_first_of('='));
 496                         if ((value.find_first_of('=')+1) <= value.length()) {
 497                                 value = value.substr(value.find_first_of('=')+1, value.length());
 498                         }
 499                 }else{
 500                         key = value;
 501                         value = 1;
 502                 }
 503         }
 504         catch(exception& e) {
 505                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 506                 exit(1);
 507         }
 508         catch(...) {
 509                 cout << "An unknown error has occurred in the GlobalData class function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 510                 exit(1);
 511         }
 512
 513 }
 514 /*******************************************************/
 515
 516 /******************************************************/