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