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; }
  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 ThreeColumnFile2::~ThreeColumnFile2(){
 110
 111         inFile.close();
 112         outFile.close();
 113         remove(outName.c_str());
 114 };
 115
 116 /***********************************************************************/
 117
 118 void ThreeColumnFile2::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 = 1; 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
 142                 outFile.setf(ios::fixed, ios::floatfield);
 143                 outFile.setf(ios::showpoint);
 144         }
 145         catch(exception& e) {
 146                 cout << "Standard Error: " << e.what() << " has occurred in the ThreeColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 147                 exit(1);
 148         }
 149         catch(...) {
 150                 cout << "An unknown error has occurred in the ThreeColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 151                 exit(1);
 152         }
 153 }
 154
 155 /***********************************************************************/
 156
 157 void ThreeColumnFile2::output(vector<double> data){
 158         try {
 159
 160                 if(counter != 0){
 161                         string inputBuffer;
 162                         getline(inFile, inputBuffer);
 163
 164                         outFile << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
 165                 }
 166                 else{
 167                         outFile << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
 168
 169                 }
 170
 171         }
 172         catch(exception& e) {
 173                 cout << "Standard Error: " << e.what() << " has occurred in the ThreeColumnFile2 class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 174                 exit(1);
 175         }
 176         catch(...) {
 177                 cout << "An unknown error has occurred in the ThreeColumnFile2 class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 178                 exit(1);
 179         }
 180 };
 181
 182 /***********************************************************************/
 183
 184 void ThreeColumnFile2::resetFile(){
 185         try {
 186                 if(counter != 0){
 187                         outFile.close();
 188                         inFile.close();
 189                 }
 190                 else{
 191                         outFile.close();
 192                 }
 193                 counter = 1;
 194
 195                 remove(inName.c_str());
 196                 renameOk = rename(outName.c_str(), inName.c_str());
 197
 198                 //checks to make sure user was able to rename and remove successfully
 199                 if ((renameOk != 0)) { cout << "Unable to rename necessary files." << endl; }
 200
 201         }
 202         catch(exception& e) {
 203                 cout << "Standard Error: " << e.what() << " has occurred in the ThreeColumnFile2 class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 204                 exit(1);
 205         }
 206         catch(...) {
 207                 cout << "An unknown error has occurred in the ThreeColumnFile2 class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 208                 exit(1);
 209         }
 210 }
 211
 212 /***********************************************************************/
 213 /***********************************************************************/
 214
 215 SharedThreeColumnFile::~SharedThreeColumnFile(){
 216
 217         inFile.close();
 218         outFile.close();
 219         remove(outName.c_str());
 220 };
 221
 222 /***********************************************************************/
 223
 224 void SharedThreeColumnFile::initFile(string label){
 225         try {
 226                 if(counter != 0){
 227                         openOutputFile(outName, outFile);
 228                         openInputFile(inName, inFile);
 229
 230                         string inputBuffer;
 231                         getline(inFile, inputBuffer);
 232
 233                         outFile <<  inputBuffer << '\t' << label << "\tlci\thci" << endl;
 234                 }
 235                 else{
 236                         openOutputFile(outName, outFile);
 237                         outFile << "numsampled\t" << groupLabel << '\t' << label << "\tlci\thci" << endl;
 238                 }
 239
 240                 outFile.setf(ios::fixed, ios::floatfield);
 241                 outFile.setf(ios::showpoint);
 242         }
 243         catch(exception& e) {
 244                 cout << "Standard Error: " << e.what() << " has occurred in the SharedThreeColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 245                 exit(1);
 246         }
 247         catch(...) {
 248                 cout << "An unknown error has occurred in the SharedThreeColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 249                 exit(1);
 250         }
 251 }
 252
 253 /***********************************************************************/
 254
 255 void SharedThreeColumnFile::output(int nSeqs, vector<double> data){
 256         try {
 257                 if(counter != 0){
 258                         string inputBuffer;
 259                         getline(inFile, inputBuffer);
 260
 261                         outFile <<  inputBuffer << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
 262                 }
 263                 else{
 264                         outFile << numGroup << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
 265                         numGroup++;
 266                 }
 267         }
 268         catch(exception& e) {
 269                 cout << "Standard Error: " << e.what() << " has occurred in the SharedThreeColumnFile class Function output. 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 SharedThreeColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 274                 exit(1);
 275         }
 276 };
 277
 278 /***********************************************************************/
 279
 280 void SharedThreeColumnFile::resetFile(){
 281         try {
 282                 if(counter != 0){
 283                         outFile.close();
 284                         inFile.close();
 285                 }
 286                 else{
 287                         outFile.close();
 288                 }
 289                 counter = 1;
 290                 remove(inName.c_str());
 291                 renameOk = rename(outName.c_str(), inName.c_str());
 292
 293                 //checks to make sure user was able to rename and remove successfully
 294                 if ((renameOk != 0)) { cout << "Unable to rename necessary files." << endl; }
 295
 296         }
 297         catch(exception& e) {
 298                 cout << "Standard Error: " << e.what() << " has occurred in the SharedThreeColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 299                 exit(1);
 300         }
 301         catch(...) {
 302                 cout << "An unknown error has occurred in the SharedThreeColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 303                 exit(1);
 304         }
 305 }
 306
 307 /***********************************************************************/
 308
 309 /***********************************************************************/
 310
 311 OneColumnFile::~OneColumnFile(){
 312
 313         inFile.close();
 314         outFile.close();
 315         remove(outName.c_str());
 316 };
 317
 318 /***********************************************************************/
 319
 320 void OneColumnFile::initFile(string label){
 321         try {
 322                 if(counter != 0){
 323                         openOutputFile(outName, outFile);
 324                         openInputFile(inName, inFile);
 325
 326                         string inputBuffer;
 327                         getline(inFile, inputBuffer);
 328
 329                         outFile <<  inputBuffer << '\t' << label << endl;
 330                 }
 331                 else{
 332                         openOutputFile(outName, outFile);
 333                         outFile << "numsequences\t" << label << endl;
 334                 }
 335
 336                 outFile.setf(ios::fixed, ios::floatfield);
 337                 outFile.setf(ios::showpoint);
 338         }
 339         catch(exception& e) {
 340                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 341                 exit(1);
 342         }
 343         catch(...) {
 344                 cout << "An unknown error has occurred in the OneColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 345                 exit(1);
 346         }
 347 }
 348
 349 /***********************************************************************/
 350
 351 void OneColumnFile::output(int nSeqs, vector<double> data){
 352         try {
 353                 if(counter != 0){
 354                         string inputBuffer;
 355                         getline(inFile, inputBuffer);
 356
 357                         outFile <<  inputBuffer << setprecision(4) << '\t'  << data[0] << endl;
 358                 }
 359                 else{
 360                         outFile << nSeqs << setprecision(4) << '\t' << data[0] << endl;
 361                 }
 362         }
 363         catch(exception& e) {
 364                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 365                 exit(1);
 366         }
 367         catch(...) {
 368                 cout << "An unknown error has occurred in the OneColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 369                 exit(1);
 370         }
 371 };
 372
 373 /***********************************************************************/
 374
 375 void OneColumnFile::resetFile(){
 376         try {
 377                 if(counter != 0){
 378                         outFile.close();
 379                         inFile.close();
 380                 }
 381                 else{
 382                         outFile.close();
 383                 }
 384                 counter = 1;
 385                 remove(inName.c_str());
 386                 renameOk = rename(outName.c_str(), inName.c_str());
 387
 388                 //checks to make sure user was able to rename and remove successfully
 389                 if ((renameOk != 0)) { cout << "Unable to rename necessary files." << endl; }
 390
 391         }
 392         catch(exception& e) {
 393                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 394                 exit(1);
 395         }
 396         catch(...) {
 397                 cout << "An unknown error has occurred in the OneColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 398                 exit(1);
 399         }
 400 }
 401
 402 /***********************************************************************/
 403 /***********************************************************************/
 404
 405 SharedOneColumnFile::~SharedOneColumnFile(){
 406
 407         inFile.close();
 408         outFile.close();
 409         remove(outName.c_str());
 410 };
 411
 412 /***********************************************************************/
 413
 414 void SharedOneColumnFile::initFile(string label){
 415         try {
 416                 if(counter != 0){
 417                         openOutputFile(outName, outFile);
 418                         openInputFile(inName, inFile);
 419
 420                         string inputBuffer;
 421                         getline(inFile, inputBuffer);
 422
 423                         outFile <<  inputBuffer << '\t' << label  << endl;
 424
 425                 }
 426                 else{
 427                         openOutputFile(outName, outFile);
 428                         outFile << "sampled\t" << label << endl;
 429
 430                 }
 431
 432                 outFile.setf(ios::fixed, ios::floatfield);
 433                 outFile.setf(ios::showpoint);
 434         }
 435         catch(exception& e) {
 436                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function initFile. 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 OneColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 441                 exit(1);
 442         }
 443 }
 444
 445 /***********************************************************************/
 446
 447 void SharedOneColumnFile::output(int nSeqs, vector<double> data){
 448         try {
 449                         string dataOutput;
 450                         float sam;
 451                         sam = data[0];
 452                         dataOutput = "";
 453                         for (int i = 0; i < data.size(); i++) {
 454                                 dataOutput = dataOutput + "\t" + toString(data[i]);
 455                         }
 456                         if(counter != 0){
 457                                 string inputBuffer;
 458                                 getline(inFile, inputBuffer);
 459
 460                                 outFile <<  inputBuffer << setprecision(2) << '\t' << dataOutput << endl;
 461                         }
 462                         else{
 463                                 outFile << nSeqs << setprecision(2) << '\t' << dataOutput << endl;
 464                         }
 465         }
 466         catch(exception& e) {
 467                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 468                 exit(1);
 469         }
 470         catch(...) {
 471                 cout << "An unknown error has occurred in the OneColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 472                 exit(1);
 473         }
 474 };
 475
 476 /***********************************************************************/
 477
 478 void SharedOneColumnFile::resetFile(){
 479         try {
 480                 if(counter != 0){
 481                         outFile.close();
 482                         inFile.close();
 483                 }
 484                 else{
 485                         outFile.close();
 486                 }
 487                 counter = 1;
 488
 489                 remove(inName.c_str());
 490                 renameOk = rename(outName.c_str(), inName.c_str());
 491
 492                 //checks to make sure user was able to rename and remove successfully
 493                 if ((renameOk != 0)) { cout << "Unable to rename necessary files." << endl; }
 494
 495
 496         }
 497         catch(exception& e) {
 498                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 499                 exit(1);
 500         }
 501         catch(...) {
 502                 cout << "An unknown error has occurred in the OneColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 503                 exit(1);
 504         }
 505 }
 506
 507 /***********************************************************************/