lib/snof.c File Reference

#include "common.h"
#include "snof.h"
#include "snofmake.h"

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Functions
void	snofClose (struct snof **pSnof)
static boolean	makeSnofName (char *snofName, char *rootName)
snof *	snofOpen (char *indexName)
snof *	snofMustOpen (char *indexName)
static long	retrieveOffset (char *item, int itemSize)
static int	snofCmp (char *prefix, char *name, int maxSize, boolean isPrefix)
static boolean	snofSearch (struct snof *snof, char *name, int nameSize, boolean isPrefix, int *pIx, char **pNameOffset)
boolean	snofFindOffset (struct snof *snof, char *name, long *pOffset)
boolean	snofFindFirstStartingWith (struct snof *snof, char *prefix, int prefixSize, int *pSnofIx)
int	snofElementCount (struct snof *snof)
long	snofOffsetAtIx (struct snof *snof, int ix)
char *	snofNameAtIx (struct snof *snof, int ix)
void	snofNameOffsetAtIx (struct snof *snof, int ix, char **pName, long *pOffset)
Variables
static char const	rcsid [] = "$Id: snof.c,v 1.4 2003/05/06 07:33:44 kate Exp $"

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Function Documentation

static boolean makeSnofName	(	char *	snofName,
		char *	rootName
	)			[static]

Definition at line 30 of file snof.c.

References ArraySize, FALSE, isSnofSig(), and TRUE.

Referenced by snofOpen().

{
static char *suffixes[2] = {".ix", ".xi"};
static char *suff = NULL;
int sigBuf[4];
FILE *f;
int i;

if (suff == NULL)
    {
    for (i=0; i<ArraySize(suffixes); ++i)
        {
        sprintf(snofName, "%s%s", rootName, suffixes[i]);
        if ((f = fopen(snofName, "rb")) != NULL)
            {
            if ((fread(sigBuf, sizeof(sigBuf), 1, f)) == 1)
                {
                if (isSnofSig(&sigBuf))
                    {
                    suff = suffixes[i];
                    }
                }
            fclose(f);
            }
        if (suff != NULL)
            break;
        }
    }
if (suff == NULL)
    return FALSE;
sprintf(snofName, "%s%s", rootName, suff);
return TRUE;
}

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static long retrieveOffset	(	char *	item,
		int	itemSize
	)			[static]

Definition at line 136 of file snof.c.

Referenced by snofFindOffset(), snofNameOffsetAtIx(), and snofOffsetAtIx().

{
unsigned offset;
memcpy(&offset, item+itemSize-sizeof(offset), sizeof(offset));
return offset;
}

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void snofClose

(

struct snof **

pSnof

)

Definition at line 15 of file snof.c.

References snof::file, snof::first, and freeMem().

Referenced by snofOpen(), wormCdnaUncache(), and wormUncacheSomeGdf().

{
struct snof *snof = *pSnof;
if (snof != NULL)
    {
    if (snof->file != NULL)
        fclose(snof->file);
    if (snof->first != NULL)
        freeMem(snof->first);
    freeMem(snof);
    *pSnof = NULL;
    }
}

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static int snofCmp	(	char *	prefix,
		char *	name,
		int	maxSize,
		boolean	isPrefix
	)			[static]

Definition at line 143 of file snof.c.

Referenced by snofFindFirstStartingWith(), and snofSearch().

{
if (isPrefix)
    return memcmp(prefix, name, maxSize);
else
    return strcmp(prefix, name);
}

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int snofElementCount

(

struct snof *

snof

)

Definition at line 263 of file snof.c.

References snof::endIx.

Referenced by findAltSpliceRange(), and wormGetSomeGdfGeneList().

{
return snof->endIx + 1;
}

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boolean snofFindFirstStartingWith	(	struct snof *	snof,
		char *	prefix,
		int	prefixSize,
		int *	pSnofIx
	)

Definition at line 241 of file snof.c.

References FALSE, snofCmp(), snofNameAtIx(), snofSearch(), and TRUE.

Referenced by findAltSpliceRange(), and wormGetSomeGdfGeneList().

{
char *nameOffset;
int matchIx;
if (!snofSearch(snof, prefix, prefixSize, TRUE,  &matchIx, &nameOffset))
    {
    *pSnofIx = matchIx; /* Pass along error code such as it is. */
    return FALSE;
    }
while (--matchIx >= 0)
    {
    nameOffset = snofNameAtIx(snof, matchIx);
    if (snofCmp(prefix, nameOffset, prefixSize, TRUE) != 0)
        break;
    }
++matchIx;
*pSnofIx = matchIx;
return TRUE;
}

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boolean snofFindOffset	(	struct snof *	snof,
		char *	name,
		long *	pOffset
	)

Definition at line 226 of file snof.c.

References FALSE, snof::itemSize, retrieveOffset(), snofSearch(), and TRUE.

Referenced by flyCdnaSeq(), wormCdnaInfo(), wormCdnaSeq(), wormGeneRange(), and wormGetSomeGdfGene().

{
char *nameOffset;
int matchIx;
if (!snofSearch(snof, name, strlen(name), FALSE,  &matchIx, &nameOffset))
    {
    *pOffset = matchIx; /* Pass along error code such as it is. */
    return FALSE;
    }
*pOffset = retrieveOffset(nameOffset, snof->itemSize);
return TRUE;
}

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struct snof* snofMustOpen

(

char *

indexName

)

[read]

Definition at line 127 of file snof.c.

References errAbort(), and snofOpen().

Referenced by flyCdnaSeq(), wormCacheSomeGdf(), wormCdnaCache(), and wormGeneRange().

{
struct snof *snof = snofOpen(indexName);
if (snof == NULL)
    errAbort("Couldn't open index file %s", indexName);
return snof;
}

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char* snofNameAtIx	(	struct snof *	snof,
		int	ix
	)

Definition at line 276 of file snof.c.

References snof::file, snof::headSize, snof::itemSize, snof::mid, and SEEK_SET.

Referenced by snofFindFirstStartingWith(), snofNameOffsetAtIx(), and snofOffsetAtIx().

{
fseek(snof->file, snof->headSize + ix*snof->itemSize, SEEK_SET);
fread(snof->mid, snof->itemSize, 1, snof->file);
return snof->mid;
}

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void snofNameOffsetAtIx	(	struct snof *	snof,
		int	ix,
		char **	pName,
		long *	pOffset
	)

Definition at line 286 of file snof.c.

References snof::itemSize, retrieveOffset(), and snofNameAtIx().

Referenced by findAltSpliceRange(), and wormGetSomeGdfGeneList().

{
char *nameOffset = snofNameAtIx(snof, ix);
*pName = nameOffset;
*pOffset = retrieveOffset(nameOffset, snof->itemSize);
}

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long snofOffsetAtIx	(	struct snof *	snof,
		int	ix
	)

Definition at line 269 of file snof.c.

References snof::itemSize, retrieveOffset(), and snofNameAtIx().

{
char *nameOffset = snofNameAtIx(snof, ix);
return retrieveOffset(nameOffset, snof->itemSize);
}

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struct snof* snofOpen

(

char *

indexName

)

[read]

Definition at line 67 of file snof.c.

References freeMem(), isSnofSig(), makeSnofName(), needMem(), SEEK_END, and snofClose().

Referenced by snofMustOpen().

{
struct snof *snof;
int sigBuf[4];
FILE *f;
char fileName[512];

if (!makeSnofName(fileName, indexName))
    return NULL;
if ((snof = needMem(sizeof(*snof))) == NULL)
    return NULL;

if ((snof->file = f = fopen(fileName, "rb")) == NULL)
    {
    freeMem(snof);
    return NULL;
    }
if ((fread(sigBuf, sizeof(sigBuf), 1, f)) != 1)
    {
    snofClose(&snof);
    return NULL;
    }
if (!isSnofSig(&sigBuf))
    {
    snofClose(&snof);
    return NULL;
    }
if ((fread(&snof->maxNameSize, sizeof(snof->maxNameSize), 1, f)) != 1)
    {
    snofClose(&snof);
    return NULL;
    }
snof->headSize = ftell(f);
snof->itemSize = snof->maxNameSize + sizeof(unsigned);
if ((snof->first = needMem(5*snof->itemSize)) == NULL)
    {
    snofClose(&snof);
    return NULL;
    }
snof->last = snof->first + snof->itemSize;
snof->less = snof->last + snof->itemSize;
snof->mid = snof->less + snof->itemSize;
snof->more = snof->mid + snof->itemSize;

if (fread(snof->first, snof->itemSize, 1, f) != 1)
    {
    snofClose(&snof);
    return NULL;
    }
fseek(f, -snof->itemSize, SEEK_END);
snof->endIx = (ftell(f)-snof->headSize)/snof->itemSize;
if (fread(snof->last, snof->itemSize, 1, f) != 1)
    {
    snofClose(&snof);
    return NULL;
    }
return snof;
}

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static boolean snofSearch	(	struct snof *	snof,
		char *	name,
		int	nameSize,
		boolean	isPrefix,
		int *	pIx,
		char **	pNameOffset
	)			[static]

Definition at line 151 of file snof.c.

References snof::endIx, FALSE, snof::file, snof::first, snof::headSize, snof::itemSize, snof::last, snof::less, snof::maxNameSize, snof::mid, snof::more, SEEK_SET, snofCmp(), and TRUE.

Referenced by snofFindFirstStartingWith(), and snofFindOffset().

 {
char *startName, *endName, *midName;
int startIx, endIx, midIx;
int cmp;
int itemSize = snof->itemSize;
FILE *f = snof->file;
int headSize = snof->headSize;

/* Truncate name size if necessary. */
if (nameSize > snof->maxNameSize)
    nameSize = snof->maxNameSize;

/* Set up endpoints of binary search */
startName = snof->less;
memcpy(startName, snof->first, itemSize);
endName = snof->more;
memcpy(endName, snof->last, itemSize);
midName = snof->mid;

startIx = 0;
endIx = snof->endIx;

/* Check for degenerate initial case */
if (snofCmp(name, startName, nameSize, isPrefix) == 0)
    {
    *pIx = startIx;
    *pNameOffset = startName;
    return TRUE;
    }
if (snofCmp(name, endName, nameSize, isPrefix) == 0)
    {
    *pIx = endIx;
    *pNameOffset =  endName;
    return TRUE;
    }

/* Do binary search. */
for (;;)
    {
    midIx = (startIx + endIx ) / 2;
    if (midIx == startIx || midIx == endIx)
        {
        *pIx = -1;
        return FALSE;
        }
    fseek(f, headSize + midIx*itemSize, SEEK_SET);
    if (fread(midName, itemSize, 1, f) < 1)
        {
        *pIx = 0;
        return FALSE;
        }
    cmp = snofCmp(name, midName, nameSize, isPrefix);
    if (cmp == 0)
        {
        *pIx = midIx;
        *pNameOffset = midName;
        return TRUE;
        }
    else if (cmp > 0)
        {
        memcpy(startName, midName, itemSize);
        startIx = midIx;
        }
    else
        {
        memcpy(endName, midName, itemSize);
        endIx = midIx;
        }
    }
}

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Variable Documentation

char const rcsid[] = "$Id: snof.c,v 1.4 2003/05/06 07:33:44 kate Exp $" [static]

Definition at line 13 of file snof.c.

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