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// $Id: nucleotide.cpp 962 2006-11-07 15:13:34Z privmane $
#include "nucleotide.h"
#include "errorMsg.h"
nucleotide::nucleotide() {
_relation.resize(4);
for (int i=0; i < _relation.size(); ++i) {
_relation[i].resize(16);
}
for (int s=0;s<4;++s) {
for (int t=0;t<16;++t){
_relation[s][t]=relationsInternal(s,t);
}
}
}
int nucleotide::fromChar(const string& str, const int pos) const {
return fromChar(str[pos]);
}
vector<int> nucleotide::fromString(const string &str) const {
vector<int> vec;
for (int i=0;i<str.size();i++)
vec.push_back(fromChar(str[i]));
return vec;
}
int nucleotide::fromChar(const char s) const {
switch (s) {
case 'A' : case'a' : return 0 ; break;// A = adenine
case 'C' : case'c' : return 1 ; break;// C = cytosine
case 'G' : case'g' : return 2 ; break;// G = guanine
case 'T' : case't' : return 3 ; break;// T = thymine
case 'U' : case'u' : return 4 ; break; // U = uracil
case 'R' : case'r' : return 5 ; break;// R = purine (same as [GA])
case 'Y' : case'y' : return 6 ; break;// Y = pyrimidine (same as [TC])
case 'K' : case'k' : return 7 ; break;// K = keto (same as [GT])
case 'M' : case'm' : return 8 ; break;// M = amino (same as [AC])
case 'S' : case's' : return 9 ; break;// S = strong (same as [GC])
case 'W' : case'w' : return 10; break;// W = weak (same as [AT])
case 'B' : case'b' : return 11; break;// B = (same as [GTC])
case 'D' : case'd' : return 12; break;// D = (same as [GAT])
case 'H' : case'h' : return 13; break;// H = (same as [ACT])
case 'V' : case'v' : return 14; break;// V = (same as [GCA])
case 'N' : case'n' : return 15; break;// N = any (same as [ACGT])
case '?' : case'*' : return 15; break;
case '-' : case'_' : return -1; break;
case 'x' : case'X' : return 15; break;
case '.' : return -3; break; // . is used in some sequence files as the character just in the line above...
default:
vector<string> err;
err.push_back(" The nucleotide sequences contained the character: ");
err[0]+=s;
err.push_back(" The nucleotide was not one of the following: ");
err.push_back("A, C, G, T, X, -, ?");
err.push_back("a, c, g, t, x, _, *");
errorMsg::reportError(err);
}
return -99;
}
string nucleotide::fromInt(const int id) const {
char x= fromIntInternal(id);
string res;
res.append(1,x);
return res;
}
char nucleotide::fromIntInternal(const int in_id) const {
switch (in_id) {
case 0 : return 'A' ; break;
case 1 : return 'C' ; break;
case 2 : return 'G' ; break;
case 3 : return 'T' ; break;
case -1: return '-' ; break;
case 4 : return 'U'; break;
case 5 : return 'R'; break;
case 6 : return 'Y'; break;
case 7 : return 'K'; break;
case 8 : return 'M'; break;
case 9 : return 'S'; break;
case 10 : return 'W'; break;
case 11 : return 'B'; break;
case 12 : return 'D'; break;
case 13 : return 'H'; break;
case 14 : return 'V'; break;
case 15 : return 'N'; break;
default:
vector<string> err;
err.push_back(" unable to print nucleotide. nucleotide was not one of the following: ");
err.push_back("A, C, G, T, -, ?");
err.push_back("a, c, g, t, _, *");
errorMsg::reportError(err); // make the program quit
}//end of switch
return '!' ; // for the lousy compiler
}
int nucleotide::relationsInternal(const int ctc,const int charInSeq
) const{ //ctc=charToCheck
switch (charInSeq){
case 0 : if (ctc==0) return 1 ; break;// A = adenine
case 1 : if (ctc==1) return 1 ; break;// C = cytosine
case 2 : if (ctc==2) return 1 ; break;// G = guanine
case 3 : if (ctc==3) return 1 ; break;// T = thymine
case 4 : if (ctc==4) return 1 ; break; // U = uracil
case 5 : if (ctc==2||ctc==0) return 1 ; break;// R = purine (same as [GA])
case 6 : if (ctc==3||ctc==1) return 1 ; break;// Y = pyrimidine (same as [TC])
case 7 : if (ctc==2||ctc==3) return 1 ; break;// K = keto (same as [GT])
case 8 : if (ctc==0||ctc==1) return 1 ; break;// M = amino (same as [AC])
case 9 : if (ctc==2||ctc==1) return 1 ; break;// S = (same as [GC])
case 10: if (ctc==0||ctc==3) return 1 ; break;// W = (same as [AT])
case 11: if (ctc==2||ctc==3||ctc==1) return 1 ; break;// B = (same as [GTC])
case 12: if (ctc==2||ctc==0||ctc==3) return 1 ; break;// D = (same as [GAT])
case 13: if (ctc==0||ctc==1||ctc==3) return 1 ; break;// H = (same as [ACT])
case 14: if (ctc==2||ctc==1||ctc==0) return 1 ; break;// V = (same as [GCA])
case 15: if (ctc==0||ctc==1||ctc==2||ctc==3) return 1 ; break;// N = any (same as [ACGT])
};
return 0;
};
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