static void
readGenBank(struct ReadSeqVars *V)
{
char *sptr;
int in_definition;
while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
getline2(V);
if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
{
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
}
in_definition = FALSE;
while (! feof(V->f))
{
getline2(V);
if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
{
if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
in_definition = TRUE;
}
else if (! feof(V->f) && strstr(V->sbuffer, "ACCESSION") == V->sbuffer)
{
if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
in_definition = FALSE;
}
else if (strncmp(V->sbuffer,"ORIGIN", 6) != 0)
{
if (in_definition)
SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
}
else
break;
}
readLoop(0, endGB, V);
/* reading a real GenBank database file, we keep the source coords
*/
V->sqinfo->start = 1;
V->sqinfo->stop = V->seqlen;
V->sqinfo->olen = V->seqlen;
V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN;
while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
getline2(V);
/* SRE: V->s now holds "//", so sequential
reads are wedged: fixed Tue Jul 13 1993 */
while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
getline2(V);
}
int main(int argc, char *argv[]) {
int length = 0;
char line[MAX_LINE_LENGTH];
int distance;
if(argc != 2 || !isnumerical(argv[1])) {
usage();
exit(EXIT_FAILURE);
} else {
distance = atoi(argv[1]);
}
while((length = getline2(line, MAX_LINE_LENGTH)) >= 0) {
if(isnumerical(line)) {
printf("%u\n", rightrot(atoi(line), distance));
} else {
exit(EXIT_FAILURE);
}
}
exit(EXIT_SUCCESS);
}
int main(int argc, char **argv)
{
char s1[MAX_LINE_LEN];
char s2[MAX_LINE_LEN];
int m, n, m2, n2;
m = DEFAULTSTARTCOL;
n = DEFAULTTABWIDTH;
while (--argc > 0) {
argv++;
if (**argv == '-') {
if ((m2 = atoi(++*argv)) > 0)
m = m2;
} else if (**argv == '+') {
if ((n2 = atoi(++*argv)) > 0)
n = n2;
}
}
printf("Usage example: entab -2 +8\n");
printf("Input some characters, then press enter:\n");
while (getline2(s1) == 0);
detab(s1, s2, m, n);
/* entab(s1, s2, m, n); */
printf("result:\n%s\n", s2);
return 0;
}
static void
readPearson(struct ReadSeqVars *V)
{
char *sptr;
if ((sptr = strtok(V->sbuffer+1, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
if ((sptr = strtok(NULL, "\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
/* workaround for long NCBI NR lines */
while (V->longline && ! feof(V->f)) getline2(V);
readLoop(0, endPearson, V);
while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
getline2(V);
}
int main() {
int len;
char line[MAXLINE];
while((len = getline2(line, MAXLINE)) > 0) {
fold(line, COLUMN);
}
}
/* Function: SeqfilePosition()
*
* Purpose: Move to a particular offset in a seqfile.
* Will not work on interleaved files (SELEX, MSF).
*/
void
SeqfilePosition(SQFILE *sqfp, long offset)
{
if (sqfp->do_stdin || sqfp->do_gzip || IsInterleavedFormat(sqfp->format))
Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
fseek(sqfp->f, offset, SEEK_SET);
getline2(sqfp);
}
static void
readZuker(struct ReadSeqVars *V)
{
char *sptr;
getline2(V); /*s == "seqLen seqid string..."*/
if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
if ((sptr = strtok(NULL, "\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
readLoop(0, endZuker, V);
while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
getline2(V);
}
int main() {
int len;
char line[MAXLINE];
char longest[MAXLINE];
while ((len = getline2(line, MAXLINE)) > 0) {
if(len > LONGLINE)
printf("\n The number of longest line is %d\n", len);
}
}
main()
{
int c;
char line[MAXLINE];
while((getline2(line, MAXLINE)) > 0)
if (remover(line) > 0)
printf("%s", line);
return 0;
}
/*wypisz wiersze dłuższe niż LONGLINE*/
main()
{
int len; /*długość bieżącego wiersza*/
char line[MAXLINE]; /*kopia bieżącego wiersza*/
while ((len = getline2(line, MAXLINE)) > 0)
if (len > LONGLINE)
printf("%s", line);
return 0;
}
static void
readEMBL(struct ReadSeqVars *V)
{
char *sptr;
/* make sure we have first line */
while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
getline2(V);
if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
{
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
}
do {
getline2(V);
if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
{
if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
}
else if (!feof(V->f) && strstr(V->sbuffer, "DE ") == V->sbuffer)
{
if ((sptr = strtok(V->sbuffer+5, "\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
}
} while (! feof(V->f) && strncmp(V->sbuffer,"SQ",2) != 0);
readLoop(0, endEMBL, V);
/* reading a real EMBL database file, we keep the source coords
*/
V->sqinfo->start = 1;
V->sqinfo->stop = V->seqlen;
V->sqinfo->olen = V->seqlen;
V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN;
/* load next record's ID line */
while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
getline2(V);
}
main() {
int len;
char line[MAXLINE];
char new_line[MAXLINE];
while ((len = getline2(line, MAXLINE)) > 0)
{
tab_replace(line, len);
printf("%s\n", line);
clear_line(line, len);
}
}
main()
{
int len;
char line[MAXLINE];
while ((len = getline2(line, MAXLINE)) > 0) {
reverse(line);
printf("%s", line);
}
return 0;
}
static void
readIG(struct ReadSeqVars *V)
{
char *nm;
/* position past ';' comments */
do {
getline2(V);
} while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
if (!feof(V->f))
{
if ((nm = strtok(V->sbuffer, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
readLoop(0, endIG, V);
}
while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
getline2(V);
}
static void
readGCGdata(struct ReadSeqVars *V)
{
int binary = FALSE; /* whether data are binary or not */
int blen; /* length of binary sequence */
/* first line contains ">>>>" followed by name */
if (Strparse(">>>>([^ ]+) .+2BIT +Len: ([0-9]+)", V->sbuffer, 2) == 0)
{
binary = TRUE;
SetSeqinfoString(V->sqinfo, sqd_parse[1], SQINFO_NAME);
blen = atoi(sqd_parse[2]);
}
else if (Strparse(">>>>([^ ]+) .+ASCII +Len: [0-9]+", V->sbuffer, 1) == 0)
SetSeqinfoString(V->sqinfo, sqd_parse[1], SQINFO_NAME);
else
Die("bogus GCGdata format? %s", V->sbuffer);
/* second line contains free text description */
getline2(V);
SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
if (binary) {
/* allocate for blen characters +3... (allow for 3 bytes of slop) */
if (blen >= V->maxseq) {
V->maxseq = blen;
if ((V->seq = (char *) realloc (V->seq, sizeof(char)*(V->maxseq+4)))==NULL)
Die("malloc failed");
}
/* read (blen+3)/4 bytes from file */
if (fread(V->seq, sizeof(char), (blen+3)/4, V->f) < (size_t) ((blen+3)/4))
Die("fread failed");
V->seqlen = blen;
/* convert binary code to seq */
GCGBinaryToSequence(V->seq, blen);
}
else readLoop(0, endGCGdata, V);
while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
getline2(V);
}
/* Function: SeqfileRewind()
*
* Purpose: Set a sequence file back to the first sequence.
* How to do this varies with whether the file is an
* unaligned file, or an alignment file for which
* we're hacking sequential access.
*/
void
SeqfileRewind(SQFILE *sqfp)
{
if (sqfp->do_stdin || sqfp->do_gzip)
Die("SeqfileRewind() failed: in a nonrewindable data file or stream");
if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
else {
rewind(sqfp->f);
getline2(sqfp);
}
}
main()
{
int len; /*current line length*/
char line[MAXLINE];
while ((len = getline2(line, MAXLINE)) > 0)
if (len > THRESHOLD) {
printf("%s", line);
printf("%d", len);
}
return 0;
}
int main()
{
char line[MAXLIMIT];
int found = 0;
while((getline2(line, MAXLIMIT)) > 0)
if((strindex(line, pattern)) >= 0) {
printf("%s", line);
found++;
}
return found;
}
static void
readPIR(struct ReadSeqVars *V)
{
char *sptr;
/* load first line of entry */
while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
getline2(V);
if (feof(V->f)) return;
if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
{
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
}
do {
getline2(V);
if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
{
if ((sptr = strtok(V->sbuffer+15, " \t\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
}
} while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
getline2(V); /* skip next line, coords */
readLoop(0, endPIR, V);
/* reading a real PIR-CODATA database file, we keep the source coords
*/
V->sqinfo->start = 1;
V->sqinfo->stop = V->seqlen;
V->sqinfo->olen = V->seqlen;
V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN;
/* get next line
*/
while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
getline2(V);
}
int main() {
int length;
char line[MAX_LINE_LENGTH];
length = 0;
while ((length = getline2(line, MAX_LINE_LENGTH)) >= 0) {
reverse(line, length);
printf("%s\n", line);
}
return 0;
}
static void
readStrider(struct ReadSeqVars *V)
{
char *nm;
while ((!feof(V->f)) && (*V->sbuffer == ';'))
{
if (strncmp(V->sbuffer,"; DNA sequence", 14) == 0)
{
if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
}
getline2(V);
}
if (! feof(V->f))
readLoop(1, endStrider, V);
/* load next line
*/
while ((!feof(V->f)) && (*V->sbuffer != ';'))
getline2(V);
}
/* print longest input line */
main()
{
int len; /* current line length */
int max; /* maximum length seen so far */
char line[MAXLINE]; /* current input line */
char longest[MAXLINE]; /* longest line saved here */
max = 0;
while ((len = getline2(line, MAXLINE)) > 0){
reverse(line,len);
printf("reversed:%s\n",line);
}
return 0;
}
main()
{
int len;
int cleaned_len;
char line[MAXLENGTH];
char longest[MAXLENGTH];
cleaned_len = 0;
while ((len = getline2(line, MAXLENGTH)) > 0)
{
if(clean(line, len) > 0)
printf("%s", line);
}
return 0;
}
main()
{
int len;
extern int max;
extern char longest[];
max = 0;
while ((len = getline2()) > 0)
if (len > max) {
max = len;
copy();
}
if (max > 0)
printf("%s", longest);
return 0;
}
int readlines(char *lineptr[], char lines[], int maxlines){
int len, totalLength, nlines;
nlines = 0;
totalLength=0;
while((len=getline2(lines, MAXLEN)) > 0){
if (nlines >= MAXLINES){
return -1;
} else {
totalLength += len;
lineptr[nlines++] = lines;
lines+=totalLength;
}
}
return nlines;
}
/* readlines: read input lines */
int readlines(char *lineptr[], char *p, int maxlines)
{
int len, nlines;
char line[MAXLEN];
nlines = 0;
while ((len = getline2(line, MAXLEN)) > 0 )
if (nlines >= maxlines)
return -1;
else {
line[len-1] = '\0'; /* delete newline */
strcpy(p, line);
lineptr[nlines++] = p;
p += len; //offseting pointer to BUF
}
return nlines;
}
/*wypisywanie najdłuższego wiersza danych wejściowych; wersja wyspecjalizowana*/
main()
{
int len;
extern int max;
extern char longest[];
max = 0;
while ((len = getline2()) > 0)
if (len > max) {
max = len;
copy();
}
if (max > 0) /*był co najmniej jeden wiersz*/
printf("%s", longest);
return 0;
}
main()
{
int len; /*current line length*/
int max; /*max length seen so far */
char line[MAXLINE]; /*current input line */
char longest[MAXLINE]; /*longest line saved here */
max = 0;
while ((len = getline2(line, MAXLINE)) > 0)
if (len > max) {
max = len;
copy(longest, line);
}
if (max > 0) /*there was a line */
printf("%s\n%d", longest, max);
return 0;
}
int main(int argc, char *argv[]) {
int sorted[MAX_VALUES];
int i, length, opt, key, result, timed = 0, iterations = 1;
char line[MAX_LINE_LENGTH];
clock_t time;
// parse command-line
while((opt = getopt(argc, argv, "tk:i:")) != -1) {
switch (opt) {
case 't':
timed = 1;
break;
case 'k':
key = atoi(optarg);
break;
case 'i':
iterations = atoi(optarg);
break;
default: /* '?' */
fprintf(stderr, "Usage: %s [-t ] [-k key]\n", argv[0]);
exit(EXIT_FAILURE);
}
}
// build the list
for(length = 0; (getline2(line, MAX_LINE_LENGTH)) >= 0 && length < MAX_VALUES; length++) {
sorted[length] = atoi(line);
}
// clocked invocation
time = clock();
for(i = 0; i < iterations; i++) {
result = binsearch(key, sorted, length);
}
time = clock() - time;
timed ? printf("%f\n", time * 1.0) : printf(":%i\n", result);
exit(EXIT_SUCCESS);
}
static void
readLoop(int addfirst, int (*endTest)(char *,int *), struct ReadSeqVars *V)
{
int addend = 0;
int done = 0;
V->seqlen = 0;
if (addfirst) addseq(V->sbuffer, V);
do {
getline2(V);
/* feof() alone is a bug; files not necessarily \n terminated */
if (*(V->sbuffer) == '\0' && feof(V->f))
done = TRUE;
done |= (*endTest)(V->sbuffer, &addend);
if (addend || !done)
addseq(V->sbuffer, V);
} while (!done);
}