inc/gfClientLib.h File Reference

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Functions
void	gfClientFileArray (char *fileName, char ***retFiles, int *retFileCount)
bioSeq *	gfClientSeqList (int fileCount, char *files[], boolean isProt, boolean isTransDna, char *maskType, float minRepDivergence, boolean showStatus)
void	gfClientUnmask (struct dnaSeq *seqList)

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Function Documentation

void gfClientFileArray	(	char *	fileName,
		char ***	retFiles,
		int *	retFileCount
	)

Definition at line 16 of file gfClientLib.c.

References AllocArray, cloneString(), FALSE, mustOpen(), nibIsFile(), readAllWords(), sameString, TRUE, and twoBitIsSpec().

Referenced by blat().

{
boolean gotSingle = FALSE;
char *buf;              /* This will leak memory but won't matter. */

if (nibIsFile(fileName) || twoBitIsSpec(fileName)
    || sameString(fileName, "stdin"))
    gotSingle = TRUE;
/* Detect .fa files (where suffix is not standardized)
 * by first character being a '>'. */
else
    {
    FILE *f = mustOpen(fileName, "r");
    char c = fgetc(f);
    fclose(f);
    if (c == '>')
        gotSingle = TRUE;
    }
if (gotSingle)
    {
    char **files;
    *retFiles = AllocArray(files, 1);
    files[0] = cloneString(fileName);
    *retFileCount = 1;
    return;
    }
else
    {
    readAllWords(fileName, retFiles, retFileCount, &buf);
    }
}

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bioSeq* gfClientSeqList	(	int	fileCount,
		char *	files[],
		boolean	isProt,
		boolean	isTransDna,
		char *	maskType,
		float	minRepDivergence,
		boolean	showStatus
	)

Definition at line 157 of file gfClientLib.c.

References doMask, faReadAllMixed(), faReadAllPep(), faToDna(), faToProtein(), maskNucSeqList(), dnaSeq::next, NIB_BASE_NAME, NIB_MASK_MIXED, nibIsFile(), nibLoadAllMasked(), slCat(), twoBitIsSpec(), twoBitLoadAll(), and ZeroVar.

Referenced by blat().

{
int i;
char *fileName;
bioSeq *seqList = NULL, *seq;
boolean doMask = (maskType != NULL);

for (i=0; i<fileCount; ++i)
    {
    struct dnaSeq *list = NULL, sseq;
    ZeroVar(&sseq);
    fileName = files[i];
    if (nibIsFile(fileName))
        list = nibLoadAllMasked(NIB_MASK_MIXED|NIB_BASE_NAME, fileName);
    else if (twoBitIsSpec(fileName))
        list = twoBitLoadAll(fileName);
    else if (isProt)
      list = faReadAllPep(fileName);
    else
      list = faReadAllMixed(fileName);

    /* If necessary mask sequence from file. */
    if (doMask)
        {
        maskNucSeqList(list, fileName, maskType, isTransDna, minRepDivergence);
        }
    else
        {
        /* If not masking send everything to proper case here. */
        for (seq = list; seq != NULL; seq = seq->next)
            {
            if (isProt)
                faToProtein(seq->dna, seq->size);
            else
                faToDna(seq->dna, seq->size);
            }
        }
    /* Move local list to end of bigger list. */
    seqList = slCat(seqList, list);
    }
if (showStatus)
    {
    /* Total up size and sequence count and report. */
    int count = 0; 
    unsigned long totalSize = 0;
    for (seq = seqList; seq != NULL; seq = seq->next)
        {
        totalSize += seq->size;
        count += 1;
        }
    printf("Loaded %lu letters in %d sequences\n", totalSize, count);
    }
return seqList;
}

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void gfClientUnmask

(

struct dnaSeq *

seqList

)

Definition at line 52 of file gfClientLib.c.

References dnaSeq::dna, faToDna(), dnaSeq::next, and dnaSeq::size.

Referenced by blat(), and maskNucSeqList().

{
struct dnaSeq *seq;
for (seq = seqList; seq != NULL; seq = seq->next)
    faToDna(seq->dna, seq->size);
}

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