inputdata.cpp

   1 /*
   2  *  inputdata.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 "inputdata.h"
  11 #include "ordervector.hpp"
  12 #include "listvector.hpp"
  13 #include "rabundvector.hpp"
  14
  15 /***********************************************************************/
  16
  17 InputData::InputData(string fName, string f) : format(f){
  18
  19         openInputFile(fName, fileHandle);
  20
  21 }
  22
  23 /***********************************************************************/
  24
  25
  26 InputData::~InputData(){
  27
  28 //      delete output;
  29
  30 }
  31
  32 /***********************************************************************/
  33
  34 InputData::InputData(string fName, string orderFileName, string f) : format(f){
  35         try {
  36
  37                 ifstream ofHandle;
  38                 openInputFile(orderFileName, ofHandle);
  39                 string name;
  40
  41                 int count = 0;
  42
  43                 while(ofHandle){
  44                         ofHandle >> name;
  45                         orderMap[name] = count;
  46                         count++;
  47                         gobble(ofHandle);
  48                 }
  49                 ofHandle.close();
  50
  51                 openInputFile(fName, fileHandle);
  52         }
  53         catch(exception& e) {
  54                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function InputData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  55                 exit(1);
  56         }
  57         catch(...) {
  58                 cout << "An unknown error has occurred in the InputData class function InputData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  59                 exit(1);
  60         }
  61 }
  62 /***********************************************************************/
  63
  64 ListVector* InputData::getListVector(){
  65         try {
  66                 if(fileHandle){
  67                         if(format == "list") {
  68                                 list = new ListVector(fileHandle);
  69                         }
  70
  71                         gobble(fileHandle);
  72                         return list;
  73                 }
  74                 else{
  75                         return 0;
  76                 }
  77         }
  78         catch(exception& e) {
  79                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  80                 exit(1);
  81         }
  82         catch(...) {
  83                 cout << "An unknown error has occurred in the InputData class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  84                 exit(1);
  85         }
  86 }
  87
  88 /***********************************************************************/
  89
  90 SharedListVector* InputData::getSharedListVector(){
  91         try {
  92                 if(fileHandle){
  93                         if (format == "shared")  {
  94                                 SharedList = new SharedListVector(fileHandle);
  95                         }
  96
  97                         gobble(fileHandle);
  98                         return SharedList;
  99                 }
 100                 else{
 101                         return 0;
 102                 }
 103         }
 104         catch(exception& e) {
 105                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 106                 exit(1);
 107         }
 108         catch(...) {
 109                 cout << "An unknown error has occurred in the InputData class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 110                 exit(1);
 111         }
 112 }
 113
 114 /***********************************************************************/
 115
 116 SharedOrderVector* InputData::getSharedOrderVector(){
 117         try {
 118                 if(fileHandle){
 119                         if (format == "sharedfile")  {
 120                                 SharedOrder = new SharedOrderVector(fileHandle);
 121                         }
 122
 123                         gobble(fileHandle);
 124                         return SharedOrder;
 125
 126                 }else{
 127                         return 0;
 128                 }
 129         }
 130         catch(exception& e) {
 131                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 132                 exit(1);
 133         }
 134         catch(...) {
 135                 cout << "An unknown error has occurred in the InputData class function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 136                 exit(1);
 137         }
 138 }
 139
 140
 141
 142 /***********************************************************************/
 143
 144 OrderVector* InputData::getOrderVector(){
 145         try {
 146                 if(fileHandle){
 147                         if(format == "list") {
 148                                 input = new ListVector(fileHandle);
 149                         }
 150                         else if (format == "shared")  {
 151                                 input = new SharedListVector(fileHandle);
 152                         }
 153                         else if(format == "rabund"){
 154                                 input = new RAbundVector(fileHandle);
 155                         }
 156                         else if(format == "order"){
 157                                 input = new OrderVector(fileHandle);
 158                         }
 159                         else if(format == "sabund"){
 160                                 input = new SAbundVector(fileHandle);
 161                         }
 162                         else if(format == "listorder"){
 163                                 input = new ListVector(fileHandle);
 164                         }
 165
 166                         gobble(fileHandle);
 167                         output = new OrderVector();
 168                         *output = (input->getOrderVector());
 169
 170                         return output;
 171                 }
 172                 else{
 173                         return 0;
 174                 }
 175         }
 176         catch(exception& e) {
 177                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 178                 exit(1);
 179         }
 180         catch(...) {
 181                 cout << "An unknown error has occurred in the InputData class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 182                 exit(1);
 183         }
 184 }
 185 /***********************************************************************/
 186 //this is used when you don't need the order vector
 187 vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(){
 188         try {
 189                 if(fileHandle){
 190                         if (format == "sharedfile")  {
 191                                 SharedRAbundVector* SharedRAbund = new SharedRAbundVector(fileHandle);
 192                                 if (SharedRAbund != NULL) {
 193                                         return SharedRAbund->getSharedRAbundVectors();
 194                                 }
 195                         }else if (format == "shared") {
 196                                 SharedList = new SharedListVector(fileHandle);
 197                                 if (SharedList != NULL) {
 198                                         return SharedList->getSharedRAbundVector();
 199                                 }
 200                         }
 201                         gobble(fileHandle);
 202                 }
 203
 204                 //this is created to signal to calling function that the input file is at eof
 205                 vector<SharedRAbundVector*> null;  null.push_back(NULL);
 206                 return null;
 207
 208         }
 209         catch(exception& e) {
 210                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getSharedRAbundVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 211                 exit(1);
 212         }
 213         catch(...) {
 214                 cout << "An unknown error has occurred in the InputData class function getSharedRAbundVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 215                 exit(1);
 216         }
 217 }
 218
 219
 220 /***********************************************************************/
 221
 222 SAbundVector* InputData::getSAbundVector(){
 223         try {
 224                 if(fileHandle){
 225                         if (format == "list") {
 226                                 input = new ListVector(fileHandle);
 227                         }
 228                         else if (format == "shared")  {
 229                                 input = new SharedListVector(fileHandle);
 230                         }
 231                         else if(format == "rabund"){
 232                                 input = new RAbundVector(fileHandle);
 233                         }
 234                         else if(format == "order"){
 235                                 input = new OrderVector(fileHandle);
 236                         }
 237                         else if(format == "sabund"){
 238                                 input = new SAbundVector(fileHandle);
 239                         }
 240
 241                         gobble(fileHandle);
 242
 243                         sabund = new SAbundVector();
 244                         *sabund = (input->getSAbundVector());
 245
 246                         return sabund;
 247                 }
 248                 else{
 249                         return 0;
 250                 }
 251         }
 252         catch(exception& e) {
 253                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 254                 exit(1);
 255         }
 256         catch(...) {
 257                 cout << "An unknown error has occurred in the InputData class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 258                 exit(1);
 259         }
 260 }
 261
 262 /***********************************************************************/
 263 RAbundVector* InputData::getRAbundVector(){
 264         try {
 265                 if(fileHandle){
 266                         if (format == "list") {
 267                                 input = new ListVector(fileHandle);
 268                         }
 269                         else if (format == "shared")  {
 270                                 input = new SharedListVector(fileHandle);
 271                         }
 272                         else if(format == "rabund"){
 273                                 input = new RAbundVector(fileHandle);
 274                         }
 275                         else if(format == "order"){
 276                                 input = new OrderVector(fileHandle);
 277                         }
 278                         else if(format == "sabund"){
 279                                 input = new SAbundVector(fileHandle);
 280                         }
 281
 282                         gobble(fileHandle);
 283
 284                         rabund = new RAbundVector();
 285                         *rabund = (input->getRAbundVector());
 286
 287                         return rabund;
 288                 }
 289                 else{
 290                         return NULL;
 291                 }
 292         }
 293         catch(exception& e) {
 294                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 295                 exit(1);
 296         }
 297         catch(...) {
 298                 cout << "An unknown error has occurred in the InputData class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 299                 exit(1);
 300         }
 301 }
 302 /***********************************************************************/
 303
 304
 305