lib/gdf.c File Reference

#include "common.h"
#include "gdf.h"

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Functions
gdfGene *	newGdfGene (char *name, int nameSize, int exonCount, char strand, UBYTE chromIx)
void	gdfFreeGene (struct gdfGene *gene)
void	gdfFreeGeneList (struct gdfGene **pList)
gdfGene *	gdfReadOneGene (FILE *f)
void	gdfGeneExtents (struct gdfGene *gene, long *pMin, long *pMax)
void	gdfOffsetGene (struct gdfGene *gene, int offset)
void	gdfRcGene (struct gdfGene *gene, int size)
void	gdfUpcExons (struct gdfGene *gene, int geneOffset, DNA *dna, int dnaSize, int dnaOffset)
Variables
static char const	rcsid [] = "$Id: gdf.c,v 1.4 2003/05/06 07:33:42 kate Exp $"

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Function Documentation

void gdfFreeGene

(

struct gdfGene *

gene

)

Definition at line 27 of file gdf.c.

References gdfGene::dataPoints, freeMem(), and gdfGene::name.

Referenced by gdfFreeGeneList(), getWormGeneDna(), getWormGeneExonDna(), and wormChromPartExonsUpper().

{
if (gene != NULL)
    {
    freeMem(gene->name);
    freeMem(gene->dataPoints);
    freeMem(gene);
    }
}

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void gdfFreeGeneList

(

struct gdfGene **

pList

)

Definition at line 38 of file gdf.c.

References gdfFreeGene(), and gdfGene::next.

{
struct gdfGene *gene, *next;
gene = *pList;
while (gene != NULL)
    {
    next = gene->next;
    gdfFreeGene(gene);
    gene = next;
    }
*pList = NULL;
}

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void gdfGeneExtents	(	struct gdfGene *	gene,
		long *	pMin,
		long *	pMax
	)

Definition at line 73 of file gdf.c.

References gdfGene::dataCount, gdfGene::dataPoints, max, min, and gdfDataPoint::start.

Referenced by gdfUpcExons(), getWormGeneDna(), and getWormGeneExonDna().

{
int i;
long x;
long min=0x7000000;
long max = -min;

for (i=0; i<gene->dataCount; i+=1)
    {
    x = gene->dataPoints[i].start;
    if (x < min)
        min = x;
    if (x > max)
        max = x;
    }
*pMin = min;
*pMax = max;
}

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void gdfOffsetGene	(	struct gdfGene *	gene,
		int	offset
	)

Definition at line 93 of file gdf.c.

References gdfGene::dataCount, gdfGene::dataPoints, and gdfDataPoint::start.

Referenced by getWormGeneDna(), and getWormGeneExonDna().

{
struct gdfDataPoint *dp = gene->dataPoints;
int count = gene->dataCount;
int i;
for (i=0; i<count; ++i)
    dp[i].start += offset;
}

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void gdfRcGene	(	struct gdfGene *	gene,
		int	size
	)

Definition at line 103 of file gdf.c.

References gdfGene::dataCount, gdfGene::dataPoints, reverseOffset(), and gdfDataPoint::start.

Referenced by getWormGeneDna(), and getWormGeneExonDna().

{
struct gdfDataPoint *s = gene->dataPoints, *e, temp;
int count = gene->dataCount;
int i;
int halfCount = count/2;


for (i=0; i<count; ++i)
    {
    s->start = reverseOffset(s->start, size) + 1;
    ++s;
    }
s = gene->dataPoints;
e = s + gene->dataCount-1;
for (i=0; i<halfCount; i += 1)
    {
    memcpy(&temp, s, sizeof(temp));
    memcpy(s, e, sizeof(temp));
    memcpy(e, &temp, sizeof(temp));
    s += 1;
    e -= 1;
    }
}

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struct gdfGene* gdfReadOneGene

(

FILE *

f

)

[read]

Definition at line 52 of file gdf.c.

References chromIx(), gdfGene::dataPoints, mustRead(), mustReadOne, newGdfGene(), gdfGene::strand, and UBYTE.

Referenced by wormGetSomeGdfGene(), and wormGetSomeGdfGeneList().

{
short pointCount;
char strand;
UBYTE geneNameSize, chromIx;
char geneNameBuf[128];
struct gdfGene *gene;

mustReadOne(f, geneNameSize);
mustRead(f, geneNameBuf, geneNameSize);
geneNameBuf[geneNameSize] = 0;
mustReadOne(f, chromIx);
mustReadOne(f, strand);
mustReadOne(f, pointCount);
gene = newGdfGene(geneNameBuf, geneNameSize, pointCount>>1, strand, chromIx);
mustRead(f, gene->dataPoints, sizeof(gene->dataPoints[0]) * pointCount);
return gene;
}

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void gdfUpcExons	(	struct gdfGene *	gene,
		int	geneOffset,
		DNA *	dna,
		int	dnaSize,
		int	dnaOffset
	)

Definition at line 131 of file gdf.c.

References gdfGene::dataCount, gdfGene::dataPoints, gdfGeneExtents(), gdfDataPoint::start, and toUpperN().

Referenced by wormChromPartExonsUpper().

{
struct gdfDataPoint *dp = gene->dataPoints;
int count = gene->dataCount;
int start, end;
long gffStart, gffEnd;
int combinedOffset;
int i;

gdfGeneExtents(gene, &gffStart, &gffEnd);
combinedOffset = -gffStart + geneOffset - dnaOffset;
for (i=0; i<count; i += 2)
    {
    start = dp[i].start + combinedOffset;
    end = dp[i+1].start + combinedOffset;
    if (end <= 0 || start >= dnaSize)
        continue;
    if (start < 0) start = 0;
    if (end > dnaSize) end = dnaSize;
    toUpperN(dna+start, end-start);
    }
}

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struct gdfGene* newGdfGene	(	char *	name,
		int	nameSize,
		int	exonCount,
		char	strand,
		UBYTE	chromIx
	)			[read]

Definition at line 11 of file gdf.c.

References cloneStringZ(), and needMem().

Referenced by gdfReadOneGene().

{
struct gdfGene *gene = needMem(sizeof *gene);
gene->name = cloneStringZ(name, nameSize);
gene->dataCount = exonCount*2;
if (exonCount > 0)
    {
    gene->dataPoints = 
            needMem(gene->dataCount * sizeof(gene->dataPoints[0]));
    }
gene->strand = strand;
gene->chromIx = chromIx;
return gene;
}

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Variable Documentation

char const rcsid[] = "$Id: gdf.c,v 1.4 2003/05/06 07:33:42 kate Exp $" [static]

Definition at line 9 of file gdf.c.

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