int main(int argc, const char * argv[]) {
const char *sentence = "He was not in the cab at the time.";
printf("\"%s\" has %d spaces \n", sentence, spaceCount(sentence));
return 0;
}
int main(int argc, const char * argv[])
{
char *word = "KC Arabit is AWESOME";
printf("\"%s\"\n" ,word);
printf("has %d number of spaces",spaceCount(word));
return 0;
}
struct lineAli *makeLineAli(char *name, struct ffAli *aliList, DNA *hay, DNA *needle, int displayOffset)
/* Make up structure showing local alignment in detail. */
{
struct lineAli *la = AllocA(struct lineAli);
int dispSize = lineSize;
DNA *dispStart = hay + displayOffset;
DNA *dispEnd = dispStart + dispSize;
int displayEndIx = displayOffset + dispSize;
struct ffAli *ali;
int i;
int startIx, endIx;
int hToN;
DNA *h, *n;
DNA nuc;
int matchCount = 0;
int totalCount = 0;
la->name = name;
memset(la->line, ' ', dispSize);
for (ali = aliList; ali != NULL; ali = ali->right)
{
if (ali->hStart >= dispEnd || ali->hEnd <= dispStart)
continue;
startIx = ali->hStart - hay;
if (startIx < displayOffset)
startIx = displayOffset;
endIx = ali->hEnd - hay;
if (endIx > displayEndIx)
endIx = displayEndIx;
hToN = ali->nStart - ali->hStart;
for (i=startIx; i<endIx; ++i)
{
h = hay+i;
n = h + hToN;
nuc = *n;
if (*h != nuc)
nuc = toupper(nuc);
else
++matchCount;
la->line[i-displayOffset] = nuc;
++totalCount;
}
}
la->score = lineSize - spaceCount(la->line);
return la;
}
int main(int argc, char* argv[]) {
char* lines1[] = {
" xxxxxxxx ",
" x x ",
" x x ",
" x x ",
"x x", //5
"x x x x",
"x xxx xxx x",
"x x x x",
"x x",
"x xxxx x", //10
"x xx x",
"x x x x",
" x xxxxxx x ",
" x x ",
" x x ", //15
" xx xx ",
" xxxx ", //17
0 };
int* image1 = makeImage(lines1);
char* lines2[] = {
"RRRRRRRRRRRR ",
"RR RR ",
"RR RR ",
"RR RR",
"RR RR", // 5
"RR RR ",
"RR RRRR ",
"RRRRRRRRRRRR ",
"RR RRR ",
"RR RR ", // 10
"RR RR ",
"RR RR",
"RR RR",
"RR RR",
" ", //15
" ",
" ", //17
0 };
int* image2 = makeImage(lines2);
char* lines3[] = { "ABC", "DEF", 0 };
int* image3 = makeImage(lines3);
char* lines4[] = {
"abcdef",
"ghijkl",
"mnopqr",
0 };
int* image4 = makeImage(lines4);
char* lines5[] = {
"A CD F",
" H K ",
"M OP R",
0 };
int* image5 = makeImage(lines5);
printf("Here is the first image:\n");
showImage(image1);
printf("Here is the second image:\n");
showImage(image2);
printf("spaces in image1: %i\n\n", spaceCount(image1));
printf("spaces in image2: %i\n\n", spaceCount(image2));
printf("Here is the third image:\n");
showImage(image3);
printf("Result of call is %d\n", f(image1, image2));
printf("Here is the first output image:\n");
showImage(image1);
printf("Here is the second output image:\n");
showImage(image2);
//printf("Here is the fourth output image:\n");
//showImage(image4);
return 0;
}
void showClump(struct ernaClump *clump, FILE *f)
/* Show detailed alignment for one clump. */
{
int chromStart = clump->start - 1000;
int chromEnd = clump->end + 1000;
int chromSize;
DNA *chromDna;
struct wormFeature *cdnaNameList, *cdnaName;
struct lineAli *laList = NULL, *la;
struct ffAli *ali;
struct dnaSeq *cdna;
boolean rcCdna;
int clumpSize = clump->end - clump->start + 1;
int displaySize = lineSize;
int displayStart = (clump->start+clump->end)/2 - displaySize/2;
int displayEnd = displayStart + displaySize;
int displayDnaOffset;
DNA *displayDna;
struct ernaHit *hit;
/* Get genomic dna and list of all cDNAs in area around clump. */
wormClipRangeToChrom(clump->chrom, &chromStart, &chromEnd);
chromSize = chromEnd - chromStart;
chromDna = wormChromPart(clump->chrom, chromStart, chromSize);
cdnaNameList = wormCdnasInRange(clump->chrom, chromStart, chromEnd);
/* Figure out 60 bases to display alignment around clump. */
wormClipRangeToChrom(clump->chrom, &displayStart, &displayEnd);
displaySize = displayEnd - displayStart;
displayDnaOffset = displayStart - chromStart;
displayDna = chromDna + displayDnaOffset;
/* Make up detailed alignment on each cDNA */
for (cdnaName = cdnaNameList; cdnaName != NULL; cdnaName = cdnaName->next)
{
struct wormCdnaInfo info;
if (!wormCdnaSeq(cdnaName->name, &cdna, &info))
{
warn("Couldn't find %s", cdnaName->name);
continue;
}
if (!ffFindEitherStrandN(cdna->dna, cdna->size, chromDna, chromSize, ffCdna, &ali, &rcCdna))
{
warn("Couldn't align %s", cdnaName->name);
continue;
}
if (rcCdna)
reverseComplement(cdna->dna, cdna->size);
la = makeLineAli(cdnaName->name, ali, chromDna, cdna->dna, displayDnaOffset);
la->isEmbryo = info.isEmbryonic;
slAddHead(&laList, la);
freeDnaSeq(&cdna);
ffFreeAli(&ali);
}
/* Display genomic with upper case at hot spots*/
displayDna[displaySize] = 0;
for (hit = clump->hits; hit != NULL; hit = hit->next)
{
int doff = hit->pos - chromStart;
chromDna[doff] = toupper(chromDna[doff]);
}
fprintf(f, "%s Genomic\n", displayDna);
/* Display aligned list by sorted score. */
slSort(&laList, cmpLaScore);
for (la = laList; la != NULL; la = la->next)
{
if (spaceCount(la->line) != lineSize)
fprintf(f, "%s %s %s\n", la->line, la->name, (la->isEmbryo ? "emb" : " "));
}
/* Clean up. */
slFreeList(&cdnaNameList);
slFreeList(&laList);
freeMem(chromDna);
}
int main(int argc, const char * argv[]) {
// Counting Space Characters in String
const char *sentence = "He was not in the cab at the time!";
printf("There are %d spaces in the sentence: %s\n", spaceCount(sentence), sentence);
return 0;
}
