fileoutput.cpp

   1 /*
   2  *  fileoutput.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 11/18/08.
   6  *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "fileoutput.h"
  11
  12 /***********************************************************************/
  13
  14 ThreeColumnFile::~ThreeColumnFile(){
  15
  16         inFile.close();
  17         outFile.close();
  18         remove(outName.c_str());
  19 };
  20
  21 /***********************************************************************/
  22
  23 void ThreeColumnFile::initFile(string label){
  24         try {
  25                 if(counter != 0){
  26                         openOutputFile(outName, outFile);
  27                         openInputFile(inName, inFile);
  28
  29                         string inputBuffer;
  30                         getline(inFile, inputBuffer);
  31
  32                         outFile <<  inputBuffer << '\t' << label << "\tlci\thci" << endl;
  33                 }
  34                 else{
  35                         openOutputFile(outName, outFile);
  36                         outFile << "numsampled\t" << label << "\tlci\thci" << endl;
  37                 }
  38
  39                 outFile.setf(ios::fixed, ios::floatfield);
  40                 outFile.setf(ios::showpoint);
  41         }
  42         catch(exception& e) {
  43                 cout << "Standard Error: " << e.what() << " has occurred in the ThreeColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  44                 exit(1);
  45         }
  46         catch(...) {
  47                 cout << "An unknown error has occurred in the ThreeColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  48                 exit(1);
  49         }
  50 }
  51
  52 /***********************************************************************/
  53
  54 void ThreeColumnFile::output(int nSeqs, vector<double> data){
  55         try {
  56                 if(counter != 0){
  57                         string inputBuffer;
  58                         getline(inFile, inputBuffer);
  59
  60                         outFile <<  inputBuffer << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
  61                 }
  62                 else{
  63                         outFile << nSeqs << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
  64                 }
  65         }
  66         catch(exception& e) {
  67                 cout << "Standard Error: " << e.what() << " has occurred in the ThreeColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  68                 exit(1);
  69         }
  70         catch(...) {
  71                 cout << "An unknown error has occurred in the ThreeColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  72                 exit(1);
  73         }
  74 };
  75
  76 /***********************************************************************/
  77
  78 void ThreeColumnFile::resetFile(){
  79         try {
  80                 if(counter != 0){
  81                         outFile.close();
  82                         inFile.close();
  83                 }
  84                 else{
  85                         outFile.close();
  86                 }
  87                 counter = 1;
  88
  89                 remove(inName.c_str());
  90                 renameOk = rename(outName.c_str(), inName.c_str());
  91
  92                 //checks to make sure user was able to rename and remove successfully
  93                 if ((renameOk != 0)) {  cout << "Unable to rename necessary files." << endl;  cout << outName << "  g   " << inName << endl;}
  94
  95         }
  96         catch(exception& e) {
  97                 cout << "Standard Error: " << e.what() << " has occurred in the ThreeColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  98                 exit(1);
  99         }
 100         catch(...) {
 101                 cout << "An unknown error has occurred in the ThreeColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 102                 exit(1);
 103         }
 104 }
 105
 106 /***********************************************************************/
 107 /***********************************************************************/
 108
 109 ColumnFile::~ColumnFile(){
 110
 111         inFile.close();
 112         outFile.close();
 113         remove(outName.c_str());
 114 };
 115
 116 /***********************************************************************/
 117
 118 void ColumnFile::initFile(string label, vector<string> tags){
 119         try {
 120                 if(counter != 0){
 121                         openOutputFile(outName, outFile);
 122                         openInputFile(inName, inFile);
 123
 124                         string inputBuffer;
 125                         getline(inFile, inputBuffer);
 126
 127                         outFile <<  inputBuffer << '\t';
 128                         for(int i = 0; i < tags.size(); i++) {
 129                                 outFile << label + tags[i] << '\t';
 130                         }
 131                         outFile << endl;
 132                 }
 133                 else{
 134                         openOutputFile(outName, outFile);
 135                         for(int i = 0; i < tags.size(); i++) {
 136                                 outFile << label + tags[i] << '\t';
 137                         }
 138                         outFile << endl;
 139                 }
 140
 141                 outFile.setf(ios::fixed, ios::floatfield);
 142                 outFile.setf(ios::showpoint);
 143         }
 144         catch(exception& e) {
 145                 cout << "Standard Error: " << e.what() << " has occurred in the ColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 146                 exit(1);
 147         }
 148         catch(...) {
 149                 cout << "An unknown error has occurred in the ColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 150                 exit(1);
 151         }
 152 }
 153
 154 /***********************************************************************/
 155
 156 void ColumnFile::output(vector<double> data){
 157         try {
 158
 159                 if(counter != 0){
 160                         string inputBuffer;
 161                         getline(inFile, inputBuffer);
 162
 163                         outFile << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length());
 164                         for (int i = 1; i< data.size(); i++) {
 165                                 outFile << '\t' << data[i];
 166                         }
 167                         outFile << endl;
 168                 }
 169                 else{
 170                         outFile << setprecision(6) << data[0] << setprecision(globaldata->getIters().length());
 171                         for (int i = 1; i< data.size(); i++) {
 172                                 outFile << '\t' << data[i];
 173                         }
 174                         outFile << endl;
 175                 }
 176
 177         }
 178         catch(exception& e) {
 179                 cout << "Standard Error: " << e.what() << " has occurred in the ColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 180                 exit(1);
 181         }
 182         catch(...) {
 183                 cout << "An unknown error has occurred in the ColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 184                 exit(1);
 185         }
 186 };
 187
 188 /***********************************************************************/
 189
 190 void ColumnFile::resetFile(){
 191         try {
 192                 if(counter != 0){
 193                         outFile.close();
 194                         inFile.close();
 195                 }
 196                 else{
 197                         outFile.close();
 198                 }
 199                 counter = 1;
 200
 201                 remove(inName.c_str());
 202                 renameOk = rename(outName.c_str(), inName.c_str());
 203
 204                 //checks to make sure user was able to rename and remove successfully
 205                 if ((renameOk != 0)) { cout << "Unable to rename necessary files." << endl; }
 206
 207         }
 208         catch(exception& e) {
 209                 cout << "Standard Error: " << e.what() << " has occurred in the ColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 210                 exit(1);
 211         }
 212         catch(...) {
 213                 cout << "An unknown error has occurred in the ColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 214                 exit(1);
 215         }
 216 }
 217
 218 /***********************************************************************/
 219 /***********************************************************************/
 220
 221 SharedThreeColumnFile::~SharedThreeColumnFile(){
 222
 223         inFile.close();
 224         outFile.close();
 225         remove(outName.c_str());
 226 };
 227
 228 /***********************************************************************/
 229
 230 void SharedThreeColumnFile::initFile(string label){
 231         try {
 232                 if(counter != 0){
 233                         openOutputFile(outName, outFile);
 234                         openInputFile(inName, inFile);
 235
 236                         string inputBuffer;
 237                         getline(inFile, inputBuffer);
 238
 239                         outFile <<  inputBuffer << '\t' << label << "\tlci\thci" << endl;
 240                 }
 241                 else{
 242                         openOutputFile(outName, outFile);
 243                         outFile << "numsampled\t" << groupLabel << '\t' << label << "\tlci\thci" << endl;
 244                 }
 245
 246                 outFile.setf(ios::fixed, ios::floatfield);
 247                 outFile.setf(ios::showpoint);
 248         }
 249         catch(exception& e) {
 250                 cout << "Standard Error: " << e.what() << " has occurred in the SharedThreeColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 251                 exit(1);
 252         }
 253         catch(...) {
 254                 cout << "An unknown error has occurred in the SharedThreeColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 255                 exit(1);
 256         }
 257 }
 258
 259 /***********************************************************************/
 260
 261 void SharedThreeColumnFile::output(int nSeqs, vector<double> data){
 262         try {
 263                 if(counter != 0){
 264                         string inputBuffer;
 265                         getline(inFile, inputBuffer);
 266
 267                         outFile <<  inputBuffer << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
 268                 }
 269                 else{
 270                         outFile << numGroup << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
 271                         numGroup++;
 272                 }
 273         }
 274         catch(exception& e) {
 275                 cout << "Standard Error: " << e.what() << " has occurred in the SharedThreeColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 276                 exit(1);
 277         }
 278         catch(...) {
 279                 cout << "An unknown error has occurred in the SharedThreeColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 280                 exit(1);
 281         }
 282 };
 283
 284 /***********************************************************************/
 285
 286 void SharedThreeColumnFile::resetFile(){
 287         try {
 288                 if(counter != 0){
 289                         outFile.close();
 290                         inFile.close();
 291                 }
 292                 else{
 293                         outFile.close();
 294                 }
 295                 counter = 1;
 296                 remove(inName.c_str());
 297                 renameOk = rename(outName.c_str(), inName.c_str());
 298
 299                 //checks to make sure user was able to rename and remove successfully
 300                 if ((renameOk != 0)) { cout << "Unable to rename necessary files." << endl; }
 301
 302         }
 303         catch(exception& e) {
 304                 cout << "Standard Error: " << e.what() << " has occurred in the SharedThreeColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 305                 exit(1);
 306         }
 307         catch(...) {
 308                 cout << "An unknown error has occurred in the SharedThreeColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 309                 exit(1);
 310         }
 311 }
 312
 313 /***********************************************************************/
 314
 315 /***********************************************************************/
 316
 317 OneColumnFile::~OneColumnFile(){
 318
 319         inFile.close();
 320         outFile.close();
 321         remove(outName.c_str());
 322 };
 323
 324 /***********************************************************************/
 325
 326 void OneColumnFile::initFile(string label){
 327         try {
 328                 if(counter != 0){
 329                         openOutputFile(outName, outFile);
 330                         openInputFile(inName, inFile);
 331
 332                         string inputBuffer;
 333                         getline(inFile, inputBuffer);
 334
 335                         outFile <<  inputBuffer << '\t' << label << endl;
 336                 }
 337                 else{
 338                         openOutputFile(outName, outFile);
 339                         outFile << "numsequences\t" << label << endl;
 340                 }
 341
 342                 outFile.setf(ios::fixed, ios::floatfield);
 343                 outFile.setf(ios::showpoint);
 344         }
 345         catch(exception& e) {
 346                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 347                 exit(1);
 348         }
 349         catch(...) {
 350                 cout << "An unknown error has occurred in the OneColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 351                 exit(1);
 352         }
 353 }
 354
 355 /***********************************************************************/
 356
 357 void OneColumnFile::output(int nSeqs, vector<double> data){
 358         try {
 359                 if(counter != 0){
 360                         string inputBuffer;
 361                         getline(inFile, inputBuffer);
 362
 363                         outFile <<  inputBuffer << setprecision(4) << '\t'  << data[0] << endl;
 364                 }
 365                 else{
 366                         outFile << nSeqs << setprecision(4) << '\t' << data[0] << endl;
 367                 }
 368         }
 369         catch(exception& e) {
 370                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 371                 exit(1);
 372         }
 373         catch(...) {
 374                 cout << "An unknown error has occurred in the OneColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 375                 exit(1);
 376         }
 377 };
 378
 379 /***********************************************************************/
 380
 381 void OneColumnFile::resetFile(){
 382         try {
 383                 if(counter != 0){
 384                         outFile.close();
 385                         inFile.close();
 386                 }
 387                 else{
 388                         outFile.close();
 389                 }
 390                 counter = 1;
 391                 remove(inName.c_str());
 392                 renameOk = rename(outName.c_str(), inName.c_str());
 393
 394                 //checks to make sure user was able to rename and remove successfully
 395                 if ((renameOk != 0)) { cout << "Unable to rename necessary files." << endl; }
 396
 397         }
 398         catch(exception& e) {
 399                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 400                 exit(1);
 401         }
 402         catch(...) {
 403                 cout << "An unknown error has occurred in the OneColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 404                 exit(1);
 405         }
 406 }
 407
 408 /***********************************************************************/
 409 /***********************************************************************/
 410
 411 SharedOneColumnFile::~SharedOneColumnFile(){
 412
 413         inFile.close();
 414         outFile.close();
 415         remove(outName.c_str());
 416 };
 417
 418 /***********************************************************************/
 419
 420 void SharedOneColumnFile::initFile(string label){
 421         try {
 422                 if(counter != 0){
 423                         openOutputFile(outName, outFile);
 424                         openInputFile(inName, inFile);
 425
 426                         string inputBuffer;
 427                         getline(inFile, inputBuffer);
 428
 429                         outFile <<  inputBuffer << '\t' << label  << endl;
 430
 431                 }
 432                 else{
 433                         openOutputFile(outName, outFile);
 434                         outFile << "sampled\t" << label << endl;
 435
 436                 }
 437
 438                 outFile.setf(ios::fixed, ios::floatfield);
 439                 outFile.setf(ios::showpoint);
 440         }
 441         catch(exception& e) {
 442                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 443                 exit(1);
 444         }
 445         catch(...) {
 446                 cout << "An unknown error has occurred in the OneColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 447                 exit(1);
 448         }
 449 }
 450
 451 /***********************************************************************/
 452
 453 void SharedOneColumnFile::output(int nSeqs, vector<double> data){
 454         try {
 455                         string dataOutput;
 456                         float sam;
 457                         sam = data[0];
 458                         dataOutput = "";
 459                         for (int i = 0; i < data.size(); i++) {
 460                                 dataOutput = dataOutput + "\t" + toString(data[i]);
 461                         }
 462                         if(counter != 0){
 463                                 string inputBuffer;
 464                                 getline(inFile, inputBuffer);
 465
 466                                 outFile <<  inputBuffer << setprecision(2) << '\t' << dataOutput << endl;
 467                         }
 468                         else{
 469                                 outFile << nSeqs << setprecision(2) << '\t' << dataOutput << endl;
 470                         }
 471         }
 472         catch(exception& e) {
 473                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 474                 exit(1);
 475         }
 476         catch(...) {
 477                 cout << "An unknown error has occurred in the OneColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 478                 exit(1);
 479         }
 480 };
 481
 482 /***********************************************************************/
 483
 484 void SharedOneColumnFile::resetFile(){
 485         try {
 486                 if(counter != 0){
 487                         outFile.close();
 488                         inFile.close();
 489                 }
 490                 else{
 491                         outFile.close();
 492                 }
 493                 counter = 1;
 494
 495                 remove(inName.c_str());
 496                 renameOk = rename(outName.c_str(), inName.c_str());
 497
 498                 //checks to make sure user was able to rename and remove successfully
 499                 if ((renameOk != 0)) { cout << "Unable to rename necessary files." << endl; }
 500
 501
 502         }
 503         catch(exception& e) {
 504                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 505                 exit(1);
 506         }
 507         catch(...) {
 508                 cout << "An unknown error has occurred in the OneColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 509                 exit(1);
 510         }
 511 }
 512
 513 /***********************************************************************/