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                 remove(inName.c_str());
  89                 rename(outName.c_str(), inName.c_str());
  90         }
  91         catch(exception& e) {
  92                 cout << "Standard Error: " << e.what() << " has occurred in the ThreeColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  93                 exit(1);
  94         }
  95         catch(...) {
  96                 cout << "An unknown error has occurred in the ThreeColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  97                 exit(1);
  98         }
  99 }
 100
 101 /***********************************************************************/
 102 /***********************************************************************/
 103
 104 SharedThreeColumnFile::~SharedThreeColumnFile(){
 105
 106         inFile.close();
 107         outFile.close();
 108         remove(outName.c_str());
 109 };
 110
 111 /***********************************************************************/
 112
 113 void SharedThreeColumnFile::initFile(string label){
 114         try {
 115                 if(counter != 0){
 116                         openOutputFile(outName, outFile);
 117                         openInputFile(inName, inFile);
 118
 119                         string inputBuffer;
 120                         getline(inFile, inputBuffer);
 121
 122                         outFile <<  inputBuffer << '\t' << label << "\tlci\thci" << endl;
 123                 }
 124                 else{
 125                         openOutputFile(outName, outFile);
 126                         outFile << "numsampled\t" << groupLabel << '\t' << label << "\tlci\thci" << endl;
 127                 }
 128
 129                 outFile.setf(ios::fixed, ios::floatfield);
 130                 outFile.setf(ios::showpoint);
 131         }
 132         catch(exception& e) {
 133                 cout << "Standard Error: " << e.what() << " has occurred in the SharedThreeColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 134                 exit(1);
 135         }
 136         catch(...) {
 137                 cout << "An unknown error has occurred in the SharedThreeColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 138                 exit(1);
 139         }
 140 }
 141
 142 /***********************************************************************/
 143
 144 void SharedThreeColumnFile::output(int nSeqs, vector<double> data){
 145         try {
 146                 if(counter != 0){
 147                         string inputBuffer;
 148                         getline(inFile, inputBuffer);
 149
 150                         outFile <<  inputBuffer << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
 151                 }
 152                 else{
 153                         outFile << numGroup << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
 154                         numGroup++;
 155                 }
 156         }
 157         catch(exception& e) {
 158                 cout << "Standard Error: " << e.what() << " has occurred in the SharedThreeColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 159                 exit(1);
 160         }
 161         catch(...) {
 162                 cout << "An unknown error has occurred in the SharedThreeColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 163                 exit(1);
 164         }
 165 };
 166
 167 /***********************************************************************/
 168
 169 void SharedThreeColumnFile::resetFile(){
 170         try {
 171                 if(counter != 0){
 172                         outFile.close();
 173                         inFile.close();
 174                 }
 175                 else{
 176                         outFile.close();
 177                 }
 178                 counter = 1;
 179                 remove(inName.c_str());
 180                 rename(outName.c_str(), inName.c_str());
 181         }
 182         catch(exception& e) {
 183                 cout << "Standard Error: " << e.what() << " has occurred in the SharedThreeColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 184                 exit(1);
 185         }
 186         catch(...) {
 187                 cout << "An unknown error has occurred in the SharedThreeColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 188                 exit(1);
 189         }
 190 }
 191
 192 /***********************************************************************/
 193
 194 /***********************************************************************/
 195
 196 OneColumnFile::~OneColumnFile(){
 197
 198         inFile.close();
 199         outFile.close();
 200         remove(outName.c_str());
 201 };
 202
 203 /***********************************************************************/
 204
 205 void OneColumnFile::initFile(string label){
 206         try {
 207                 if(counter != 0){
 208                         openOutputFile(outName, outFile);
 209                         openInputFile(inName, inFile);
 210
 211                         string inputBuffer;
 212                         getline(inFile, inputBuffer);
 213
 214                         outFile <<  inputBuffer << '\t' << label << endl;
 215                 }
 216                 else{
 217                         openOutputFile(outName, outFile);
 218                         outFile << "numsequences\t" << label << endl;
 219                 }
 220
 221                 outFile.setf(ios::fixed, ios::floatfield);
 222                 outFile.setf(ios::showpoint);
 223         }
 224         catch(exception& e) {
 225                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 226                 exit(1);
 227         }
 228         catch(...) {
 229                 cout << "An unknown error has occurred in the OneColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 230                 exit(1);
 231         }
 232 }
 233
 234 /***********************************************************************/
 235
 236 void OneColumnFile::output(int nSeqs, vector<double> data){
 237         try {
 238                 if(counter != 0){
 239                         string inputBuffer;
 240                         getline(inFile, inputBuffer);
 241
 242                         outFile <<  inputBuffer << setprecision(4) << '\t'  << data[0] << endl;
 243                 }
 244                 else{
 245                         outFile << nSeqs << setprecision(4) << '\t' << data[0] << endl;
 246                 }
 247         }
 248         catch(exception& e) {
 249                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 250                 exit(1);
 251         }
 252         catch(...) {
 253                 cout << "An unknown error has occurred in the OneColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 254                 exit(1);
 255         }
 256 };
 257
 258 /***********************************************************************/
 259
 260 void OneColumnFile::resetFile(){
 261         try {
 262                 if(counter != 0){
 263                         outFile.close();
 264                         inFile.close();
 265                 }
 266                 else{
 267                         outFile.close();
 268                 }
 269                 counter = 1;
 270                 remove(inName.c_str());
 271                 rename(outName.c_str(), inName.c_str());
 272         }
 273         catch(exception& e) {
 274                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function resetFile. 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 OneColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 279                 exit(1);
 280         }
 281 }
 282
 283 /***********************************************************************/
 284 /***********************************************************************/
 285
 286 SharedOneColumnFile::~OneColumnFile(){
 287
 288         inFile.close();
 289         outFile.close();
 290         remove(outName.c_str());
 291 };
 292
 293 /***********************************************************************/
 294
 295 void SharedOneColumnFile::initFile(string label){
 296         try {
 297                 if(counter != 0){
 298                         openOutputFile(outName, outFile);
 299                         openInputFile(inName, inFile);
 300
 301                         string inputBuffer;
 302                         getline(inFile, inputBuffer);
 303
 304                         outFile <<  inputBuffer << '\t' << label  << endl;
 305
 306                 }
 307                 else{
 308                         openOutputFile(outName, outFile);
 309                         outFile << "sampled\t" << label << endl;
 310
 311                 }
 312
 313                 outFile.setf(ios::fixed, ios::floatfield);
 314                 outFile.setf(ios::showpoint);
 315         }
 316         catch(exception& e) {
 317                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 318                 exit(1);
 319         }
 320         catch(...) {
 321                 cout << "An unknown error has occurred in the OneColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 322                 exit(1);
 323         }
 324 }
 325
 326 /***********************************************************************/
 327
 328 void SharedOneColumnFile::output(int nSeqs, vector<double> data){
 329         try {
 330                         string dataOutput;
 331                         float sam;
 332                         sam = data[0];
 333                         dataOutput = "";
 334                         for (int i = 0; i < data.size(); i++) {
 335                                 dataOutput = dataOutput + "\t" + toString(data[i]);
 336                         }
 337                         if(counter != 0){
 338                                 string inputBuffer;
 339                                 getline(inFile, inputBuffer);
 340
 341                                 outFile <<  inputBuffer << setprecision(2) << '\t' << dataOutput << endl;
 342                         }
 343                         else{
 344                                 outFile << nSeqs << setprecision(2) << '\t' << dataOutput << endl;
 345                         }
 346         }
 347         catch(exception& e) {
 348                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 349                 exit(1);
 350         }
 351         catch(...) {
 352                 cout << "An unknown error has occurred in the OneColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 353                 exit(1);
 354         }
 355 };
 356
 357 /***********************************************************************/
 358
 359 void SharedOneColumnFile::resetFile(){
 360         try {
 361                 if(counter != 0){
 362                         outFile.close();
 363                         inFile.close();
 364                 }
 365                 else{
 366                         outFile.close();
 367                 }
 368                 counter = 1;
 369                 remove(inName.c_str());
 370                 rename(outName.c_str(), inName.c_str());
 371         }
 372         catch(exception& e) {
 373                 cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 374                 exit(1);
 375         }
 376         catch(...) {
 377                 cout << "An unknown error has occurred in the OneColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 378                 exit(1);
 379         }
 380 }
 381
 382 /***********************************************************************/