lib/xa.c File Reference

#include "common.h"
#include "sig.h"
#include "xa.h"

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Functions
void	xaAliFree (struct xaAli *xa)
void	xaAliFreeList (struct xaAli **pXa)
int	xaAliCmpTarget (const void *va, const void *vb)
FILE *	xaOpenVerify (char *fileName)
FILE *	xaIxOpenVerify (char *fileName)
static void	eatLf (FILE *f)
static void	eatThroughLf (FILE *f)
xaAli *	xaReadNext (FILE *f, boolean condensed)
xaAli *	xaRdRange (FILE *ix, FILE *data, int start, int end, boolean condensed)
xaAli *	xaReadRange (char *rangeIndexFileName, char *dataFileName, int start, int end, boolean condensed)
char *	xaAlignSuffix ()
char *	xaChromIxSuffix ()
Variables
static char const	rcsid [] = "$Id: xa.c,v 1.5 2003/05/06 07:33:44 kate Exp $"

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Function Documentation

static void eatLf

(

FILE *

f

)

[static]

Definition at line 67 of file xa.c.

References errAbort().

Referenced by xaReadNext().

{
int c;
c = fgetc(f);
if (c == '\r')
    c = fgetc(f);
if (c != '\n')
    errAbort("Expecting new line in cross-species alignment file.");
}

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static void eatThroughLf

(

FILE *

f

)

[static]

Definition at line 78 of file xa.c.

Referenced by xaReadNext().

{
int c;
while ((c = fgetc(f)) != EOF)
    if (c == '\n')
        break;
}

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int xaAliCmpTarget	(	const void *	va,
		const void *	vb
	)

Definition at line 35 of file xa.c.

References xaAli::target, and xaAli::tStart.

{
const struct xaAli *a = *((struct xaAli **)va);
const struct xaAli *b = *((struct xaAli **)vb);
int diff;
if ((diff = strcmp(a->target, b->target)) == 0)
    diff = a->tStart - b->tStart;
return diff;
}

void xaAliFree

(

struct xaAli *

xa

)

Definition at line 11 of file xa.c.

References freeMem(), xaAli::hSym, xaAli::name, xaAli::qSym, xaAli::query, xaAli::target, and xaAli::tSym.

Referenced by xaAliFreeList().

{
freeMem(xa->name);
freeMem(xa->query);
freeMem(xa->target);
freeMem(xa->qSym);
freeMem(xa->tSym);
freeMem(xa->hSym);
freeMem(xa);
}

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void xaAliFreeList

(

struct xaAli **

pXa

)

Definition at line 23 of file xa.c.

References xaAli::next, and xaAliFree().

{
struct xaAli *xa, *next;
for (xa = *pXa; xa != NULL; xa = next)
    {
    next = xa->next;
    xaAliFree(xa);
    }
*pXa = NULL;
}

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char* xaAlignSuffix

(

)

Definition at line 217 of file xa.c.

{
return ".st";
}

char* xaChromIxSuffix

(

)

Definition at line 223 of file xa.c.

{
return ".xao";
}

FILE* xaIxOpenVerify

(

char *

fileName

)

Definition at line 55 of file xa.c.

References bits32, errAbort(), mustOpen(), mustReadOne, and xaoSig.

Referenced by xaReadRange().

{
FILE *f;
bits32 sig;
f = mustOpen(fileName, "rb");
mustReadOne(f, sig);
if (sig != xaoSig)
    errAbort("Bad signature on %s", fileName);
return f;
}

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FILE* xaOpenVerify

(

char *

fileName

)

Definition at line 47 of file xa.c.

References mustOpen().

Referenced by xaReadRange().

{
FILE *f = mustOpen(fileName, "rb");
return f;
}

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struct xaAli* xaRdRange	(	FILE *	ix,
		FILE *	data,
		int	start,
		int	end,
		boolean	condensed
	)			[read]

Definition at line 166 of file xa.c.

References bits32, max, min, mustReadOne, readOne, SEEK_SET, slAddHead, slReverse(), and xaReadNext().

Referenced by xaReadRange().

{
int s, e;
int maxS, minE;
long offset;
struct xaAli *list = NULL, *xa;


/* Scan through index file looking for things in range.
 * When find one read it from data file and add it to list. */
fseek(ix, sizeof(bits32), SEEK_SET);
for (;;)
    {
    if (!readOne(ix, s))
        break;
    mustReadOne(ix, e);
    mustReadOne(ix, offset);
    if (s >= end)
        break;
    maxS = max(s, start);
    minE = min(e, end);
    if (minE - maxS > 0)
        {
        fseek(data, offset, SEEK_SET);
        xa = xaReadNext(data, condensed);
        slAddHead(&list, xa);
        }
    }

slReverse(&list);
return list;
}

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struct xaAli* xaReadNext	(	FILE *	f,
		boolean	condensed
	)			[read]

Definition at line 92 of file xa.c.

References AllocVar, ArraySize, chopLine, chopString(), cloneString(), eatLf(), eatThroughLf(), errAbort(), xaAli::hSym, xaAli::milliScore, mustRead(), xaAli::name, needMem(), newOffset(), xaAli::qEnd, xaAli::qStart, xaAli::qStrand, xaAli::qSym, xaAli::query, round, sameString, xaAli::symCount, xaAli::target, xaAli::tEnd, xaAli::tStart, xaAli::tStrand, and xaAli::tSym.

Referenced by xaRdRange().

{
char line[512];
char *words[16];
int wordCount;
struct xaAli *xa;
char *parts[5];
int partCount;
double percentScore;
int symCount;
int newOffset = 0;
char *s, *e;

/* Get first line and parse out everything but the sym lines. */
if (fgets(line, sizeof(line), f) == NULL)
    return NULL;
wordCount = chopLine(line, words);
if (wordCount < 9)
    errAbort("Short line in cross-species alignment file");
if (wordCount == 10)
    newOffset = 1;
if (!sameString(words[1], "align"))
    errAbort("Bad line in cross-species alignment file");
AllocVar(xa);
xa->name = cloneString(words[0]);
s = words[5+newOffset];
e = strrchr(s, ':');
if (e == NULL)
    errAbort("Bad line (no colon) in cross-species alignment file");
*e++ = 0;
partCount = chopString(e, "-", parts, ArraySize(parts));
if (partCount != 2)
    errAbort("Bad range format in cross-species alignment file");
if (!condensed)
    xa->query = cloneString(s);
xa->qStart = atoi(parts[0]);
xa->qEnd = atoi(parts[1]);
xa->qStrand = words[6+newOffset][0];
partCount = chopString(words[7+newOffset], ":-", parts, ArraySize(parts));
if (!condensed)
    xa->target = cloneString(parts[0]);
xa->tStart = atoi(parts[1]);
xa->tEnd = atoi(parts[2]);
xa->tStrand = words[8+newOffset][0];
percentScore = atof(words[2]);
xa->milliScore = round(percentScore*10);    
xa->symCount = symCount = atoi(words[4]);

/* Get symbol lines. */
if (condensed)
    {
    eatThroughLf(f);
    eatThroughLf(f);
    eatThroughLf(f);
    }
else
    {
    xa->qSym = needMem(symCount+1);
    mustRead(f, xa->qSym, symCount);
    eatLf(f);

    xa->tSym = needMem(symCount+1);
    mustRead(f, xa->tSym, symCount);
    eatLf(f);

    xa->hSym = needMem(symCount+1);
    mustRead(f, xa->hSym, symCount);
    eatLf(f);
    }
return xa;
}

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struct xaAli* xaReadRange	(	char *	rangeIndexFileName,
		char *	dataFileName,
		int	start,
		int	end,
		boolean	condensed
	)			[read]

Definition at line 203 of file xa.c.

References xaIxOpenVerify(), xaOpenVerify(), and xaRdRange().

{
FILE *ix = xaIxOpenVerify(rangeIndexFileName);
FILE *data = xaOpenVerify(dataFileName);
struct xaAli *xa = xaRdRange(ix, data, start, end, condensed);
fclose(data);
fclose(ix);
return xa;
}

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Variable Documentation

char const rcsid[] = "$Id: xa.c,v 1.5 2003/05/06 07:33:44 kate Exp $" [static]

Definition at line 9 of file xa.c.

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