readfasta.cpp

   1 /*
   2  *  readfasta.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 4/21/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "readfasta.h"
  11 #include <iostream>
  12 #include <fstream>
  13
  14 /*******************************************************************************/
  15 ReadFasta::ReadFasta(string file) : ReadSeqs(file) {}
  16 /*******************************************************************************/
  17 ReadFasta::~ReadFasta(){
  18         //for(int i = 0; i < sequencedb.getNumSeqs(); i++)
  19                 //delete sequencedb.get(i);
  20 }
  21 /*******************************************************************************/
  22 void ReadFasta::read() {
  23         try {
  24         /*string name = "";
  25         string sequence = "";
  26         string temp;
  27         int count = 0;
  28
  29         while(!filehandle.eof()){
  30                 if(count == 0)
  31                         filehandle >> temp;
  32                 if(temp.substr(0,1).compare(">") == 0) {
  33                         if(count != 0) {
  34                                 Sequence newSequence(name, sequence);
  35                                 sequencedb.add(newSequence);
  36                                 sequence = "";
  37                         }
  38                         else
  39                                 count++;
  40                         name = temp.substr(1,temp.length()-1);
  41                 }
  42                 else {
  43                         sequence += temp;
  44                 }
  45
  46                 filehandle >> temp;
  47                 gobble(filehandle);
  48
  49                 if(filehandle.eof())
  50                         sequence += temp;
  51
  52         }
  53         Sequence newSequence(name, sequence);
  54         sequencedb.add(newSequence); */
  55
  56                 string name, sequence, line;
  57                 sequence = "";
  58                 int c;
  59                 string temp;
  60
  61
  62                 //read through file
  63                 while ((c = filehandle.get()) != EOF) {
  64                         name = ""; sequence = "";
  65                         //is this a name
  66                         if (c == '>') {
  67                                 name = readName(filehandle);
  68                                 sequence = readSequence(filehandle);
  69                         }else {  cout << "Error fasta in your file. Please correct." << endl; }
  70
  71                         //input sequence info into sequencedb
  72                         Sequence newSequence(name, sequence);
  73                         sequencedb.add(newSequence);
  74
  75                         //takes care of white space
  76                         gobble(filehandle);
  77                 }
  78
  79                 filehandle.close();
  80         }
  81         catch(exception& e) {
  82                 cout << "Standard Error: " << e.what() << " has occurred in the ReadFasta class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  83                 exit(1);
  84         }
  85         catch(...) {
  86                 cout << "An unknown error has occurred in the ReadFasta class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  87                 exit(1);
  88         }
  89 }
  90
  91 /*********************************************************************************/
  92 SequenceDB* ReadFasta::getDB() {
  93         return &sequencedb;
  94 }
  95 /*******************************************************************************/
  96 string ReadFasta::readName(ifstream& in) {
  97         try{
  98                 string name = "";
  99                 int c;
 100                 string temp;
 101
 102                 while ((c = in.get()) != EOF) {
 103                         //if c is not a line return
 104                         if (c != 10) {
 105                                 name += c;
 106                         }else { break;  }
 107                 }
 108
 109                 return name;
 110         }
 111         catch(exception& e) {
 112                 cout << "Standard Error: " << e.what() << " has occurred in the ReadFasta class Function readName. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 113                 exit(1);
 114         }
 115         catch(...) {
 116                 cout << "An unknown error has occurred in the ReadFasta class function readName. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 117                 exit(1);
 118         }
 119 }
 120
 121 /*******************************************************************************/
 122 string ReadFasta::readSequence(ifstream& in) {
 123         try{
 124                 string sequence = "";
 125                 string line;
 126                 int pos, c;
 127
 128                 while (!in.eof()) {
 129                         //save position in file in case next line is a new name.
 130                         pos = in.tellg();
 131                         line = "";
 132                         in >> line;
 133                         //if you are at a new name
 134                         if (line[0] == '>') {
 135                                 //put file pointer back since you are now at a new name
 136                                 in.seekg(pos, ios::beg);
 137                                 c = in.get();  //because you put it back to a newline char
 138                                 break;
 139                         }else {  sequence += line;      }
 140                 }
 141
 142                 return sequence;
 143         }
 144         catch(exception& e) {
 145                 cout << "Standard Error: " << e.what() << " has occurred in the ReadFasta class Function readSequence. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 146                 exit(1);
 147         }
 148         catch(...) {
 149                 cout << "An unknown error has occurred in the ReadFasta class function readSequence. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 150                 exit(1);
 151         }
 152 }
 153 /*******************************************************************************/
 154