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// =============================================================== //
// //
// File : adRevCompl.cxx //
// Purpose : reverse / complement nucleotide sequences //
// //
// Coded by Ralf Westram (coder@reallysoft.de) in January 2001 //
// Institute of Microbiology (Technical University Munich) //
// http://www.arb-home.de/ //
// //
// =============================================================== //
#include "arbdbt.h"
#include <cctype>
static char GBT_complementNucleotide(char c, char T_or_U) {
char n = c;
switch (c)
{
case 'A': n = T_or_U; break; // A <-> TU
case 'a': n = tolower(T_or_U); break;
case 'U':
case 'T': n = 'A'; break;
case 'u':
case 't': n = 'a'; break;
case 'C': n = 'G'; break; // C <-> G
case 'c': n = 'g'; break;
case 'G': n = 'C'; break;
case 'g': n = 'c'; break;
case 'M': n = 'K'; break; // M=A/C <-> TU/G=K
case 'm': n = 'k'; break;
case 'K': n = 'M'; break;
case 'k': n = 'm'; break;
case 'R': n = 'Y'; break; // R=A/G <-> TU/C=Y
case 'r': n = 'y'; break;
case 'Y': n = 'R'; break;
case 'y': n = 'r'; break;
case 'V': n = 'B'; break; // V=A/C/G <-> TU/G/C=B
case 'v': n = 'b'; break;
case 'B': n = 'V'; break;
case 'b': n = 'v'; break;
case 'H': n = 'D'; break; // H=A/C/TU <-> TU/G/A=D
case 'h': n = 'd'; break;
case 'D': n = 'H'; break;
case 'd': n = 'h'; break;
case 'S': // S = C/G <-> G/C=S
case 's':
case 'W': // W = A/TU <-> TU/A=W
case 'w':
case 'N': // N = A/C/G/TU
case 'n':
case '.':
case '-': break;
default: break;
}
return n;
}
char *GBT_reverseNucSequence(const char *s, int len) {
char *n = (char*)malloc(len+1);
int p;
if (!n) {
GB_memerr();
return 0;
}
len--;
for (p=0; len>=0; p++, len--) {
n[p] = s[len];
}
n[p] = 0;
return n;
}
char *GBT_complementNucSequence(const char *s, int len, char T_or_U) {
char *n = (char*)malloc(len+1);
int p;
for (p=0; p<len; p++) {
n[p] = GBT_complementNucleotide(s[p], T_or_U);
}
n[p] = 0;
return n;
}
NOT4PERL GB_ERROR GBT_determine_T_or_U(GB_alignment_type alignment_type, char *T_or_U, const char *supposed_target) {
switch (alignment_type)
{
case GB_AT_RNA: *T_or_U = 'U'; break;
case GB_AT_DNA: *T_or_U = 'T'; break;
default: {
*T_or_U = 0;
return GBS_global_string("%s not available for alignment-type", supposed_target);
}
}
return 0;
}
NOT4PERL void GBT_reverseComplementNucSequence(char *seq, long length, char T_or_U) {
long i, l;
for (i=0, l=length-1; i <= l; i++, l--) {
char c = seq[i];
seq[i] = GBT_complementNucleotide(seq[l], T_or_U);
seq[l] = GBT_complementNucleotide(c, T_or_U);
}
}
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