gclib/gclib/gdna.cpp

#include "gdna.h"
#include <string.h>

#define IUPAC_DEFS "AaCcTtGgUuMmRrWwSsYyKkVvHhDdBbNnXx-*"
#define IUPAC_COMP "TtGgAaCcAaKkYyWwSsRrMmBbDdHhVvNnXx-*"

unsigned char ntCompTable[256];

static bool gdna_ntCompTableReady=ntCompTableInit();

char ntComplement(char c) {
 return ntCompTable[(int)c];
 }

//in place reverse complement of nucleotide (sub)sequence
char* reverseComplement(char* seq, int slen) {
   if (slen==0) slen=strlen(seq);
   //reverseChars(seq,len);
   int l=0;
   int r=slen-1;
   register char c;
   while (l<r) {
      c=seq[l];seq[l]=seq[r];
      seq[r]=c;   //this was: Gswap(str[l],str[r]);
      l++;r--;
      }
   for (int i=0;i<slen;i++) seq[i]=ntComplement(seq[i]);
   return seq;
 }

bool ntCompTableInit() {
       //if (gdna_ntCompTableReady) return true;
       char n[]=IUPAC_DEFS;
       char c[]=IUPAC_COMP;
       int l=strlen(IUPAC_DEFS);
       ntCompTable[0]=0;
       for (int ch=1;ch<256;ch++) {
          ntCompTable[ch]=0;
          for (int i=0;i<l;i++)
                if (ch==n[i]) {
                  ntCompTable[ch]=c[i];
                  break;
                  }
          if (ntCompTable[ch]==0)
              ntCompTable[ch]='N';
          }
      //gdna_ntCompTableReady=true;
      return true;
     }
Revision:	144
Committed:	Thu Dec 22 19:15:46 2011 UTC (12 years, 8 months ago) by gpertea
File size:	1267 byte(s)
Log Message:	added GBitVec.h; removed operator> requirement for sorted vectors; swap() is now template Gswap()
Line	User	Rev	File contents
1	gpertea	2	#include "gdna.h"
2			#include <string.h>
3
4			#define IUPAC_DEFS "AaCcTtGgUuMmRrWwSsYyKkVvHhDdBbNnXx-*"
5			#define IUPAC_COMP "TtGgAaCcAaKkYyWwSsRrMmBbDdHhVvNnXx-*"
6
7			unsigned char ntCompTable[256];
8
9			static bool gdna_ntCompTableReady=ntCompTableInit();
10
11			char ntComplement(char c) {
12			return ntCompTable[(int)c];
13			}
14
15			//in place reverse complement of nucleotide (sub)sequence
16			char* reverseComplement(char* seq, int slen) {
17			if (slen==0) slen=strlen(seq);
18			//reverseChars(seq,len);
19			int l=0;
20			int r=slen-1;
21			register char c;
22			while (l<r) {
23			c=seq[l];seq[l]=seq[r];
24	gpertea	144	seq[r]=c; //this was: Gswap(str[l],str[r]);
25	gpertea	2	l++;r--;
26			}
27			for (int i=0;i<slen;i++) seq[i]=ntComplement(seq[i]);
28			return seq;
29			}
30
31			bool ntCompTableInit() {
32			//if (gdna_ntCompTableReady) return true;
33			char n[]=IUPAC_DEFS;
34			char c[]=IUPAC_COMP;
35			int l=strlen(IUPAC_DEFS);
36			ntCompTable[0]=0;
37			for (int ch=1;ch<256;ch++) {
38			ntCompTable[ch]=0;
39			for (int i=0;i<l;i++)
40			if (ch==n[i]) {
41			ntCompTable[ch]=c[i];
42			break;
43			}
44			if (ntCompTable[ch]==0)
45			ntCompTable[ch]='N';
46			}
47			//gdna_ntCompTableReady=true;
48			return true;
49			}