inc/localmem.h File Reference

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Defines
#define	lmAllocVar(lm, pt)   (pt = lmAlloc(lm, sizeof(*pt)));
#define	lmAllocArray(lm, pt, size)   (pt = lmAlloc(lm, sizeof(*pt) * (size)))
Functions
lm *	lmInit (int blockSize)
void	lmCleanup (struct lm **pLm)
void *	lmAlloc (struct lm *lm, size_t size)
char *	lmCloneString (struct lm *lm, char *string)
slName *	lmSlName (struct lm *lm, char *name)
void *	lmCloneMem (struct lm *lm, void *pt, size_t size)

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Define Documentation

#define lmAllocArray	(	lm,
		pt,
		size		)	(pt = lmAlloc(lm, sizeof(*pt) * (size)))

Definition at line 35 of file localmem.h.

Referenced by bandExt(), and ffFindExtendNmers().

#define lmAllocVar	(	lm,
		pt		)	(pt = lmAlloc(lm, sizeof(*pt)));

Definition at line 31 of file localmem.h.

Referenced by boxFindClumps(), chainBlocks(), ffAliFromSym(), ffFindExtendNmers(), getHitsFromServer(), gfFastFindDnaHits(), gfSegmentedFindHits(), gfSegmentedFindNearHits(), gfStraightFindHits(), gfStraightFindNearHits(), kdBuild(), kdTreeMake(), pslQueryGet(), rBoxJoin(), rbTreeAdd(), ssFindBestBig(), and twoBitOpen().

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Function Documentation

void* lmAlloc	(	struct lm *	lm,
		size_t	size
	)

Definition at line 78 of file localmem.c.

References lm::allignAdd, lm::allignMask, lm::blocks, lmBlock::end, lmBlock::free, lm, and newBlock().

Referenced by ffNeedMem(), gffNeedMem(), hashAddN(), lmCloneMem(), lmCloneString(), lmSlName(), localNeedMem(), newFofRecEl(), newHash(), pslLoadLm(), pslxLoadLm(), and rbTreeNew().

{
struct lmBlock *mb = lm->blocks;
void *ret;
size_t memLeft = mb->end - mb->free;
if (memLeft < size)
    mb = newBlock(lm, size);
ret = mb->free;
mb->free += ((size+lm->allignAdd)&lm->allignMask);
if (mb->free > mb->end)
    mb->free = mb->end;
return ret;
}

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void lmCleanup

(

struct lm **

pLm

)

Definition at line 67 of file localmem.c.

References lm::blocks, freeMem(), lm, and slFreeList().

Referenced by bandExt(), chainBlocks(), cleanupMem(), dnaQuery(), ffMemCleanup(), fofMake(), freeHash(), genoFindDirect(), gfAlignTrans(), gfAlignTransTrans(), gffClose(), gfFindAlignAaTrans(), gfTransTransFindBundles(), rbTreeFree(), searchOneProt(), ssFindBestBig(), transQuery(), and transTransQuery().

{
    struct lm *lm = *pLm;
    if (lm == NULL)
        return;
    slFreeList(&lm->blocks);
    freeMem(lm);
    *pLm = NULL;
}

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void* lmCloneMem	(	struct lm *	lm,
		void *	pt,
		size_t	size
	)

Definition at line 93 of file localmem.c.

References lm, and lmAlloc().

Referenced by rangeTreeAdd().

{
void *d = lmAlloc(lm, size);
memcpy(d, pt, size);
return d;
}

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char* lmCloneString	(	struct lm *	lm,
		char *	string
	)

Definition at line 101 of file localmem.c.

References lm, and lmAlloc().

Referenced by hashTwoColumnFile(), pslLoadLm(), pslxLoadLm(), raFoldInOneRetName(), raFromString(), and raNextRecord().

{
if (string == NULL)
    return NULL;
else
    {
    int size = strlen(string)+1;
    char *s = lmAlloc(lm, size);
    memcpy(s, string, size);
    return s;
    }
}

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struct lm* lmInit

(

int

blockSize

)

[read]

Definition at line 47 of file localmem.c.

References lm, needMem(), and newBlock().

Referenced by bandExt(), boxFindClumps(), chainBlocks(), dnaQuery(), ffFindExtendNmers(), ffMemInit(), fofMake(), genoFindDirect(), gfAlignTrans(), gfAlignTransTrans(), gfFindAlignAaTrans(), gffOpen(), gfLongDnaInMem(), gfTransTransFindBundles(), initMem(), newHash(), rbTreeNew(), searchOneProt(), ssFindBestBig(), transQuery(), and transTransQuery().

{
struct lm *lm;
int aliSize = sizeof(long);
if (aliSize < sizeof(double))
    aliSize = sizeof(double);
if (aliSize < sizeof(void *))
    aliSize = sizeof(void *);
lm = needMem(sizeof(*lm));
lm->blocks = NULL;
if (blockSize <= 0)
    blockSize = (1<<14);    /* 16k default. */
lm->blockSize = blockSize;
lm->allignAdd = (aliSize-1);
lm->allignMask = ~lm->allignAdd;
newBlock(lm, blockSize);
return lm;
}

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struct slName* lmSlName	(	struct lm *	lm,
		char *	name
	)			[read]

Definition at line 115 of file localmem.c.

References lm, lmAlloc(), and slName::name.

{
struct slName *n;
int size = sizeof(*n) + strlen(name) + 1;
n = lmAlloc(lm, size);
strcpy(n->name, name);
return n;
}

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