sequence.cpp

   1 /*
   2  *  sequence.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 12/15/08.
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 using namespace std;
  11
  12 #include <string>
  13 #include <fstream>
  14
  15 #include "sequence.hpp"
  16
  17 //********************************************************************************************************************
  18
  19 Sequence::Sequence(){}
  20
  21 //********************************************************************************************************************
  22
  23 Sequence::Sequence(ifstream& fastaFile){
  24
  25         string accession;
  26         fastaFile >> accession;
  27         setName(accession);
  28
  29         char letter;
  30         string sequence;
  31
  32         while(fastaFile && letter != '>'){
  33
  34                 letter = fastaFile.get();
  35
  36                 if(isalpha(letter)){
  37
  38                         sequence += letter;
  39
  40                 }
  41
  42         }
  43         fastaFile.putback(letter);
  44
  45         if(sequence.find_first_of('-') != string::npos){
  46                 setAligned(sequence);
  47         }
  48         setUnaligned(sequence);
  49 }
  50
  51
  52 //********************************************************************************************************************
  53
  54 string Sequence::convert2ints(){
  55
  56         if(unaligned == "")     {       /* need to throw an error */    }
  57
  58         string processed;
  59
  60         for(int i=0;i<unaligned.length();i++){
  61                 if(toupper(unaligned[i]) == 'A')                        {       processed += '0';       }
  62                 else if(toupper(unaligned[i]) == 'C')   {       processed += '1';       }
  63                 else if(toupper(unaligned[i]) == 'G')   {       processed += '2';       }
  64                 else if(toupper(unaligned[i]) == 'T')   {       processed += '3';       }
  65                 else if(toupper(unaligned[i]) == 'U')   {       processed += '3';       }
  66                 else                                                                    {       processed += '4';       }
  67         }
  68         return processed;
  69 }
  70
  71 //********************************************************************************************************************
  72
  73 void Sequence::setName(string seqName){
  74         if(seqName[0] == '>')   {       name = seqName.substr(1);       }
  75         else                                    {       name = seqName;                         }
  76 }
  77
  78 //********************************************************************************************************************
  79
  80 void Sequence::setUnaligned(string sequence){
  81
  82         if(sequence.find_first_of('-') != string::npos){
  83                 string temp = "";
  84                 for(int j=0;j<sequence.length();j++){
  85                         if(isalpha(sequence[j]))        {       temp += sequence[j];    }
  86                 }
  87                 unaligned = temp;
  88         }
  89         else{
  90                 unaligned = sequence;
  91         }
  92
  93 }
  94
  95 //********************************************************************************************************************
  96
  97 void Sequence::setAligned(string sequence){
  98         aligned = sequence;
  99 }
 100
 101 //********************************************************************************************************************
 102
 103 void Sequence::setPairwise(string sequence){
 104         pairwise = sequence;
 105 }
 106
 107 //********************************************************************************************************************
 108
 109 string Sequence::getSeqName(){
 110         return name;
 111 }
 112
 113 //********************************************************************************************************************
 114
 115 string Sequence::getAligned(){
 116         return aligned;
 117 }
 118
 119 //********************************************************************************************************************
 120
 121 string Sequence::getPairwise(){
 122         return pairwise;
 123 }
 124
 125 //********************************************************************************************************************
 126
 127 string Sequence::getUnaligned(){
 128         return unaligned;
 129 }
 130
 131 //********************************************************************************************************************