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") || (format == "shared")){
  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 /***********************************************************************/
  90
  91 OrderVector* InputData::getOrderVector(){
  92         try {
  93                 if(fileHandle){
  94                         if((format == "list") || (format == "shared")){
  95                                 input = new ListVector(fileHandle);
  96                         }
  97                         else if(format == "rabund"){
  98                                 input = new RAbundVector(fileHandle);
  99                         }
 100                         else if(format == "order"){
 101                                 input = new OrderVector(fileHandle);
 102                         }
 103                         else if(format == "sabund"){
 104                                 input = new SAbundVector(fileHandle);
 105                         }
 106                         else if(format == "listorder"){
 107                                 input = new ListVector(fileHandle);
 108                         }
 109
 110                         gobble(fileHandle);
 111                         output = new OrderVector();
 112                         *output = (input->getOrderVector());
 113                         //delete input;
 114                         return output;
 115                 }
 116                 else{
 117                         return 0;
 118                 }
 119         }
 120         catch(exception& e) {
 121                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 122                 exit(1);
 123         }
 124         catch(...) {
 125                 cout << "An unknown error has occurred in the InputData class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 126                 exit(1);
 127         }
 128 }
 129
 130 /***********************************************************************/
 131
 132 SAbundVector* InputData::getSAbundVector(){
 133         try {
 134                 if(fileHandle){
 135                         if((format == "list") || (format == "shared")){
 136                                 input = new ListVector(fileHandle);
 137                         }
 138                         else if(format == "rabund"){
 139                                 input = new RAbundVector(fileHandle);
 140                         }
 141                         else if(format == "order"){
 142                                 input = new OrderVector(fileHandle);
 143                         }
 144                         else if(format == "sabund"){
 145                                 input = new SAbundVector(fileHandle);
 146                         }
 147
 148                         gobble(fileHandle);
 149
 150                         sabund = new SAbundVector();
 151                         *sabund = (input->getSAbundVector());
 152
 153                         return sabund;
 154                 }
 155                 else{
 156                         return 0;
 157                 }
 158         }
 159         catch(exception& e) {
 160                 cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 161                 exit(1);
 162         }
 163         catch(...) {
 164                 cout << "An unknown error has occurred in the InputData class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 165                 exit(1);
 166         }
 167 }
 168
 169 /***********************************************************************/