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