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
  14 /***********************************************************************/
  15
  16 InputData::InputData(string fName, string f) : format(f){
  17
  18         openInputFile(fName, fileHandle);
  19
  20 }
  21
  22 /***********************************************************************/
  23
  24
  25 InputData::~InputData(){
  26
  27 //      delete output;
  28
  29 }
  30
  31 /***********************************************************************/
  32
  33 InputData::InputData(string fName, string orderFileName, string f) : format(f){
  34         try {
  35
  36                 ifstream ofHandle;
  37                 openInputFile(orderFileName, ofHandle);
  38                 string name;
  39
  40                 int count = 0;
  41
  42                 while(ofHandle){
  43                         ofHandle >> name;
  44                         orderMap[name] = count;
  45                         count++;
  46                         gobble(ofHandle);
  47                 }
  48                 ofHandle.close();
  49
  50                 openInputFile(fName, fileHandle);
  51         }
  52         catch(exception& e) {
  53                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function InputData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  54                 exit(1);
  55         }
  56         catch(...) {
  57                 cout << "An unknown error has occurred in the InputData class function InputData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  58                 exit(1);
  59         }
  60 }
  61 /***********************************************************************/
  62
  63 ListVector* InputData::getListVector(){
  64         try {
  65                 if(fileHandle){
  66                         if(format == "list") {
  67                                 list = new ListVector(fileHandle);
  68                         }
  69
  70                         gobble(fileHandle);
  71                         return list;
  72                 }
  73                 else{
  74                         return 0;
  75                 }
  76         }
  77         catch(exception& e) {
  78                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  79                 exit(1);
  80         }
  81         catch(...) {
  82                 cout << "An unknown error has occurred in the InputData class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  83                 exit(1);
  84         }
  85 }
  86
  87 /***********************************************************************/
  88
  89 SharedListVector* InputData::getSharedListVector(){
  90         try {
  91                 if(fileHandle){
  92                         if (format == "shared")  {
  93                                 SharedList = new SharedListVector(fileHandle);
  94                         }
  95
  96                         gobble(fileHandle);
  97                         return SharedList;
  98                 }
  99                 else{
 100                         return 0;
 101                 }
 102         }
 103         catch(exception& e) {
 104                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 105                 exit(1);
 106         }
 107         catch(...) {
 108                 cout << "An unknown error has occurred in the InputData class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 109                 exit(1);
 110         }
 111 }
 112
 113 /***********************************************************************/
 114
 115 SharedOrderVector* InputData::getSharedOrderVector(){
 116         try {
 117                 if(fileHandle){
 118                         if (format == "sharedfile")  {
 119                                 SharedOrder = new SharedOrderVector(fileHandle);
 120                         }
 121
 122                         gobble(fileHandle);
 123                         return SharedOrder;
 124
 125                 }else{
 126                         return 0;
 127                 }
 128         }
 129         catch(exception& e) {
 130                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 131                 exit(1);
 132         }
 133         catch(...) {
 134                 cout << "An unknown error has occurred in the InputData class function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 135                 exit(1);
 136         }
 137 }
 138
 139
 140
 141 /***********************************************************************/
 142
 143 OrderVector* InputData::getOrderVector(){
 144         try {
 145                 if(fileHandle){
 146                         if(format == "list") {
 147                                 input = new ListVector(fileHandle);
 148                         }
 149                         else if (format == "shared")  {
 150                                 input = new SharedListVector(fileHandle);
 151                         }
 152                         else if(format == "rabund"){
 153                                 input = new RAbundVector(fileHandle);
 154                         }
 155                         else if(format == "order"){
 156                                 input = new OrderVector(fileHandle);
 157                         }
 158                         else if(format == "sabund"){
 159                                 input = new SAbundVector(fileHandle);
 160                         }
 161                         else if(format == "listorder"){
 162                                 input = new ListVector(fileHandle);
 163                         }
 164
 165                         gobble(fileHandle);
 166                         output = new OrderVector();
 167                         *output = (input->getOrderVector());
 168
 169                         return output;
 170                 }
 171                 else{
 172                         return 0;
 173                 }
 174         }
 175         catch(exception& e) {
 176                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 177                 exit(1);
 178         }
 179         catch(...) {
 180                 cout << "An unknown error has occurred in the InputData class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 181                 exit(1);
 182         }
 183 }
 184
 185 /***********************************************************************/
 186
 187 SAbundVector* InputData::getSAbundVector(){
 188         try {
 189                 if(fileHandle){
 190                         if (format == "list") {
 191                                 input = new ListVector(fileHandle);
 192                         }
 193                         else if (format == "shared")  {
 194                                 input = new SharedListVector(fileHandle);
 195                         }
 196                         else if(format == "rabund"){
 197                                 input = new RAbundVector(fileHandle);
 198                         }
 199                         else if(format == "order"){
 200                                 input = new OrderVector(fileHandle);
 201                         }
 202                         else if(format == "sabund"){
 203                                 input = new SAbundVector(fileHandle);
 204                         }
 205
 206                         gobble(fileHandle);
 207
 208                         sabund = new SAbundVector();
 209                         *sabund = (input->getSAbundVector());
 210
 211                         return sabund;
 212                 }
 213                 else{
 214                         return 0;
 215                 }
 216         }
 217         catch(exception& e) {
 218                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 219                 exit(1);
 220         }
 221         catch(...) {
 222                 cout << "An unknown error has occurred in the InputData class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 223                 exit(1);
 224         }
 225 }
 226
 227 /***********************************************************************/