void nothingness ()
{
int * _i = NULL;
int * i = nullptr;
int _j = NULL;
//int j = nullptr; // ERROR!!!
if (ambig(0)) { } // ambig(int)
if (ambig(NULL)) { } // ambig(int) when NULL=0
// ambiguous when NULL=0L
if (ambig(nullptr)) { } // ambig(char*)
}
/* int checkRevEnd()
* Checks the seq for a match of the reverse primer
* at the 3' end.
*/
int checkRevEnd(char* seq, char* rev, int misAllow,
int revSt, int revEnd) {
int primEnd = strlen(rev) - 1;
int seqEnd = strlen(seq) - 1;
// allow primer to match starting at diff. positions
for (int off = revSt; off < revEnd; off++) {
int mis = misAllow;
int j;
for (j = 0; j < primEnd + 1; j++) {
int seqPos = seqEnd - j - off;
int pos = primEnd - j;
if (j + off < 0)
continue;
else if (seqPos < 0 ||
(rev[pos] != seq[seqPos] &&
(rev[pos] == 'A' || rev[pos] == 'C' ||
rev[pos] == 'G' || rev[pos] == 'T' ||
ambig(rev[pos], seq[seqPos])) && --mis < 0))
break;
}
if (j == primEnd + 1) {
return seqEnd - j - off + 1; // last base of primer
}
}
return 0;
}
/* Primer* findPrim(char*)
* Finds a primer match to the given sequence.
*/
Primer* findPrim(char* seq, int misAllow, int fwdSt, int fwdEnd,
int* st, int* f) {
for (Primer* p = primo; p != NULL; p = p->next) {
for (int i = 0; i < 2; i++) {
char* prim = (i ? p->rrc : p->fwd);
// allow primer to match starting at diff. positions
for (int off = fwdSt; off < fwdEnd; off++) {
int mis = misAllow;
int j;
for (j = 0; prim[j] != '\0'; j++)
if (j + off < 0)
continue;
else if (seq[j+off] == '\0' ||
(prim[j] != seq[j+off] &&
(prim[j] == 'A' || prim[j] == 'C' ||
prim[j] == 'G' || prim[j] == 'T' ||
ambig(prim[j], seq[j+off])) && --mis < 0))
break;
if (prim[j] == '\0') {
if (seq[j+off] != '\0') {
*st = j+off;
*f = i;
return p;
} else
return NULL;
}
}
}
}
return NULL;
}
/* -------------------------------------------------------------------- */
void tutorial(char *filename)
{
int i;
char temp[14];
char oldverbose;
outFlag = OUTOK;
setio(whichIO, echo, outFlag);
if (!expert) mPrintf("\n <3J0>ump <3N0>ext <3P0>ause <3S0>top\n");
/* doCR(); */
if (changedir(cfg.helppath) == -1 ) return;
/* no bad files */
if (checkfilename(filename, 0) == ERROR)
{
mPrintf(" No helpfile %s", filename);
changedir(cfg.homepath);
return;
}
if (ambig(filename))
{
/* fill our directory array according to filename */
oldverbose = verbose;
verbose = FALSE;
filldirectory(filename);
verbose = oldverbose;
/* print out all the files */
for (i = 0; filedir[i].entry[0] &&
( dumpf(filedir[i].entry) != ERROR) ; i++);
if ( !i) mPrintf(" No helpfile %s", filename);
/* free file directory structure */
if(filedir != NULL)
_ffree((void *)filedir);
}
else
{
strcpy(temp, filename);
temp[strlen(temp)-1] = '@';
if (filexists(temp) && *term.bold)
dump(temp);
else
dumpf(filename);
}
/* go to our home-path */
changedir(cfg.homepath);
}
/* int checkRevInt()
* Checks the seq for a match of the reverse primer
* internally.
*/
int checkRevInt(char* seq, char* rev, int st,
int misAllow, int len) {
int last = strlen(seq) - len + 1;
for (int i = st; i < last; i++) {
int mis = misAllow;
int j;
for (j = 0; j < len; j++)
if (rev[j] != seq[i + j] &&
(rev[j] == 'A' || rev[j] == 'C' ||
rev[j] == 'G' || rev[j] == 'T' ||
ambig(rev[j], seq[i + j])) && --mis < 0)
break;
if (j == len)
return i;
}
return 0;
}
/* int checkRevLen()
* Checks the seq for a match of the reverse primer
* based on the expected amplicon length.
*/
int checkRevLen(char* seq, char* rev, int st,
int bedSt, int bedEnd) {
// check only the 3' fragment, do not allow mismatches
// allow primer to match starting at diff. positions
int len = strlen(seq);
for (int off = bedSt; off < bedEnd; off++) {
if (st+off >= len)
break;
int j;
for (j = 0; rev[j] != '\0' && seq[st+j+off] != '\0'; j++)
if (rev[j] != seq[st+j+off] &&
(rev[j] == 'A' || rev[j] == 'C' ||
rev[j] == 'G' || rev[j] == 'T' ||
ambig(rev[j], seq[st+j+off])))
break;
if (rev[j] == '\0' || seq[st+j+off] == '\0')
return st+off;
}
return 0;
}
