mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 03:10:26 +08:00
123 lines
4.6 KiB
C++
123 lines
4.6 KiB
C++
// $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;
|
|
};
|
|
|