gclib/tophat_cpp/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:	154
Committed:	Tue Jan 24 02:29:21 2012 UTC (12 years, 7 months ago) by gpertea
File size:	1267 byte(s)
Log Message:	massive update with Daehwan's work
Line	File contents
1	#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	seq[r]=c; //this was: Gswap(str[l],str[r]);
25	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	}