inputdata.cpp

   1 /*
   2  *  inputdata.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 11/18/08.
   6  *  Copyright 2008 __MyCompanyName__. All rights reserved.
   7  *
   8  */
   9
  10 #include "inputdata.h"
  11 #include "ordervector.hpp"
  12 #include "listvector.hpp"
  13 #include "utilities.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                 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
 116 OrderVector* InputData::getOrderVector(){
 117         try {
 118                 if(fileHandle){
 119                         if(format == "list") {
 120                                 input = new ListVector(fileHandle);
 121                         }
 122                         else if(format == "shared") {
 123                                 input = new SharedListVector(fileHandle);
 124                         }
 125                         else if(format == "rabund"){
 126                                 input = new RAbundVector(fileHandle);
 127                         }
 128                         else if(format == "order"){
 129                                 input = new OrderVector(fileHandle);
 130                         }
 131                         else if(format == "sabund"){
 132                                 input = new SAbundVector(fileHandle);
 133                         }
 134                         else if(format == "listorder"){
 135                                 input = new ListVector(fileHandle);
 136                         }
 137
 138                         gobble(fileHandle);
 139                         output = new OrderVector();
 140                         *output = (input->getOrderVector());
 141                         //delete input;
 142                         return output;
 143                 }
 144                 else{
 145                         return 0;
 146                 }
 147         }
 148         catch(exception& e) {
 149                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 150                 exit(1);
 151         }
 152         catch(...) {
 153                 cout << "An unknown error has occurred in the InputData class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 154                 exit(1);
 155         }
 156 }
 157
 158 /***********************************************************************/
 159
 160 SAbundVector* InputData::getSAbundVector(){
 161         try {
 162                 if(fileHandle){
 163                         if (format == "list") {
 164                                 input = new ListVector(fileHandle);
 165                         }
 166                         else if(format == "shared") {
 167                                 input = new SharedListVector(fileHandle);
 168                         }
 169                         else if(format == "rabund"){
 170                                 input = new RAbundVector(fileHandle);
 171                         }
 172                         else if(format == "order"){
 173                                 input = new OrderVector(fileHandle);
 174                         }
 175                         else if(format == "sabund"){
 176                                 input = new SAbundVector(fileHandle);
 177                         }
 178
 179                         gobble(fileHandle);
 180
 181                         sabund = new SAbundVector();
 182                         *sabund = (input->getSAbundVector());
 183
 184                         return sabund;
 185                 }
 186                 else{
 187                         return 0;
 188                 }
 189         }
 190         catch(exception& e) {
 191                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 192                 exit(1);
 193         }
 194         catch(...) {
 195                 cout << "An unknown error has occurred in the InputData class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 196                 exit(1);
 197         }
 198 }
 199
 200 /***********************************************************************/