lib/localmem.c File Reference

#include "common.h"
#include "localmem.h"

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Data Structures
struct	lm
struct	lmBlock
Functions
static struct lmBlock *	newBlock (struct lm *lm, size_t reqSize)
lm *	lmInit (int blockSize)
void	lmCleanup (struct lm **pLm)
void *	lmAlloc (struct lm *lm, size_t size)
void *	lmCloneMem (struct lm *lm, void *pt, size_t size)
char *	lmCloneString (struct lm *lm, char *string)
slName *	lmSlName (struct lm *lm, char *name)
Variables
static char const	rcsid [] = "$Id: localmem.c,v 1.10 2005/04/11 07:20:03 markd Exp $"

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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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static struct lmBlock* newBlock	(	struct lm *	lm,
		size_t	reqSize
	)			[static, read]

Definition at line 32 of file localmem.c.

References lm::blocks, lm::blockSize, lmBlock::end, errAbort(), lmBlock::free, lm, needLargeZeroedMem(), and lmBlock::next.

Referenced by lmAlloc(), and lmInit().

{
size_t size = (reqSize > lm->blockSize ? reqSize : lm->blockSize);
size_t fullSize = size + sizeof(struct lmBlock);
struct lmBlock *mb = needLargeZeroedMem(fullSize);
if (mb == NULL)
    errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
mb->free = (char *)(mb+1);
mb->end = ((char *)mb) + fullSize;
mb->next = lm->blocks;
lm->blocks = mb;
return mb;
}

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Variable Documentation

char const rcsid[] = "$Id: localmem.c,v 1.10 2005/04/11 07:20:03 markd Exp $" [static]

Definition at line 14 of file localmem.c.

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