lib/nibTwo.c File Reference

#include "common.h"
#include "hash.h"
#include "dnaseq.h"
#include "nib.h"
#include "twoBit.h"
#include "nibTwo.h"

Include dependency graph for nibTwo.c:

Go to the source code of this file.

Functions
nibTwoCache *	nibTwoCacheNew (char *pathName)
void	nibTwoCacheFree (struct nibTwoCache **pNtc)
dnaSeq *	nibTwoCacheSeq (struct nibTwoCache *ntc, char *seqName)
dnaSeq *	nibTwoCacheSeqPartExt (struct nibTwoCache *ntc, char *seqName, int start, int size, boolean doMask, int *retFullSeqSize)
dnaSeq *	nibTwoCacheSeqPart (struct nibTwoCache *ntc, char *seqName, int start, int size, int *retFullSeqSize)
dnaSeq *	nibTwoLoadOne (char *pathName, char *seqName)
Variables
static char const	rcsid [] = "$Id: nibTwo.c,v 1.5 2006/03/10 17:43:37 angie Exp $"

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Function Documentation

void nibTwoCacheFree

(

struct nibTwoCache **

pNtc

)

Definition at line 28 of file nibTwo.c.

References freez(), hashElFreeList(), hashElListHash(), hashFree, nibTwoCache::isTwoBit, hashEl::next, nibTwoCache::nibHash, nibInfoFree(), nibTwoCache::pathName, nibTwoCache::tbf, twoBitClose(), and hashEl::val.

{
struct nibTwoCache *ntc = *pNtc;
if (ntc != NULL)
    {
    freez(&ntc->pathName);
    if (ntc->isTwoBit)
        twoBitClose(&ntc->tbf);
    else
        {
        struct hashEl *el, *list = hashElListHash(ntc->nibHash);
        struct nibInfo *nib;
        for (el = list; el != NULL; el = el->next)
             {
             nib = el->val;
             nibInfoFree(&nib);
             }
        hashElFreeList(&list);
        hashFree(&ntc->nibHash);
        }
    freez(pNtc);
    }
}

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struct nibTwoCache* nibTwoCacheNew

(

char *

pathName

)

[read]

Definition at line 13 of file nibTwo.c.

References AllocVar, cloneString(), nibTwoCache::isTwoBit, newHash(), nibTwoCache::nibHash, nibTwoCache::pathName, nibTwoCache::tbf, twoBitIsFile(), and twoBitOpen().

{
struct nibTwoCache *ntc;
AllocVar(ntc);
ntc->pathName = cloneString(pathName);
ntc->isTwoBit = twoBitIsFile(pathName);
if (ntc->isTwoBit)
    ntc->tbf = twoBitOpen(pathName);
else
    ntc->nibHash = newHash(10);
return ntc;
}

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struct dnaSeq* nibTwoCacheSeq	(	struct nibTwoCache *	ntc,
		char *	seqName
	)			[read]

Definition at line 53 of file nibTwo.c.

References nibInfo::f, nibInfo::fileName, nibTwoCache::isTwoBit, nibTwoCache::nibHash, nibInfoFromCache(), nibLdPart(), nibTwoCache::pathName, nibInfo::size, nibTwoCache::tbf, and twoBitReadSeqFrag().

{
if (ntc->isTwoBit)
    return twoBitReadSeqFrag(ntc->tbf, seqName, 0, 0);
else
    {
    struct nibInfo *nib = nibInfoFromCache(ntc->nibHash, ntc->pathName, seqName);
    return nibLdPart(nib->fileName, nib->f, nib->size, 0, nib->size);
    }
}

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struct dnaSeq* nibTwoCacheSeqPart	(	struct nibTwoCache *	ntc,
		char *	seqName,
		int	start,
		int	size,
		int *	retFullSeqSize
	)			[read]

Definition at line 87 of file nibTwo.c.

References nibTwoCacheSeqPartExt(), and TRUE.

{
return nibTwoCacheSeqPartExt(ntc, seqName, start, size, TRUE, retFullSeqSize);
}

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struct dnaSeq* nibTwoCacheSeqPartExt	(	struct nibTwoCache *	ntc,
		char *	seqName,
		int	start,
		int	size,
		boolean	doMask,
		int *	retFullSeqSize
	)			[read]

Definition at line 65 of file nibTwo.c.

References nibInfo::f, nibInfo::fileName, nibTwoCache::isTwoBit, NIB_MASK_MIXED, nibTwoCache::nibHash, nibInfoFromCache(), nibLdPartMasked(), nibTwoCache::pathName, nibInfo::size, nibTwoCache::tbf, and twoBitReadSeqFragExt().

Referenced by nibTwoCacheSeqPart().

{
if (ntc->isTwoBit)
    {
    return twoBitReadSeqFragExt(ntc->tbf, seqName, start, start+size,
                                doMask, retFullSeqSize);
    }
else
    {
    struct nibInfo *nib = nibInfoFromCache(ntc->nibHash, ntc->pathName, seqName);
    int opts = (doMask ? NIB_MASK_MIXED : 0);
    if (retFullSeqSize != NULL)
        *retFullSeqSize = nib->size;
    return nibLdPartMasked(opts, nib->fileName, nib->f, nib->size, start, size);
    }
}

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struct dnaSeq* nibTwoLoadOne	(	char *	pathName,
		char *	seqName
	)			[read]

Definition at line 95 of file nibTwo.c.

References NIB_MASK_MIXED, nibLoadAllMasked(), safef(), twoBitClose(), twoBitIsFile(), twoBitOpen(), and twoBitReadSeqFrag().

{
struct dnaSeq *seq;
if (twoBitIsFile(pathName))
    {
    struct twoBitFile *tbf = twoBitOpen(pathName);
    seq = twoBitReadSeqFrag(tbf, seqName, 0, 0);
    twoBitClose(&tbf);
    }
else
    {
    char path[512];
    safef(path, sizeof(path), "%s/%s.nib", pathName, seqName);
    seq = nibLoadAllMasked(NIB_MASK_MIXED, path);
    }
return seq;
}

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Variable Documentation

char const rcsid[] = "$Id: nibTwo.c,v 1.5 2006/03/10 17:43:37 angie Exp $" [static]

Definition at line 11 of file nibTwo.c.

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