lib/ffScore.c File Reference

#include "common.h"
#include "dnautil.h"
#include "obscure.h"
#include "fuzzyFind.h"

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Functions
void	setFfIntronMax (int value)
int	ffScoreMatch (DNA *a, DNA *b, int size)
int	ffCalcCdnaGapPenalty (int hGap, int nGap)
static int	calcTightGap (int hGap, int nGap)
static int	calcLooseGap (int hGap, int nGap)
int	ffCalcGapPenalty (int hGap, int nGap, enum ffStringency stringency)
int	ffCdnaGapPenalty (struct ffAli *left, struct ffAli *right)
int	ffGapPenalty (struct ffAli *left, struct ffAli *right, enum ffStringency stringency)
int	ffScoreSomeAlis (struct ffAli *ali, int count, enum ffStringency stringency)
int	ffScoreSomething (struct ffAli *ali, enum ffStringency stringency, boolean isProt)
int	ffScore (struct ffAli *ali, enum ffStringency stringency)
int	ffScoreCdna (struct ffAli *ali)
int	ffScoreProtein (struct ffAli *ali, enum ffStringency stringency)
Variables
static char const	rcsid [] = "$Id: ffScore.c,v 1.5 2003/10/21 22:06:32 kent Exp $"
int	ffIntronMax = ffIntronMaxDefault

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Function Documentation

static int calcLooseGap	(	int	hGap,
		int	nGap
	)			[static]

Definition at line 93 of file ffScore.c.

References min.

Referenced by ffCalcGapPenalty().

{
if (hGap == 0 && nGap == 0)
    return 0;
else
    {
    int overlap = min(hGap, nGap);
    int penalty = 8;
    if (overlap < 0)
        overlap = 0;

    if (hGap < 0)
        hGap = -8*hGap;
    if (nGap < 0)
        nGap = -2*nGap;
    penalty += log(hGap-overlap+1) + log(nGap-overlap+1);
    return penalty;
    }
}

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static int calcTightGap	(	int	hGap,
		int	nGap
	)			[static]

Definition at line 72 of file ffScore.c.

References min.

Referenced by ffCalcGapPenalty().

{
if (hGap == 0 && nGap == 0)
    return 0;
else
    {
    int overlap = min(hGap, nGap);
    int penalty = 8;
    if (overlap < 0)
        overlap = 0;

    if (hGap < 0)
        hGap = -8*hGap;
    if (nGap < 0)
        nGap = -2*nGap;
    penalty += (hGap-overlap + nGap-overlap) + overlap;
    return penalty;
    }
}

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int ffCalcCdnaGapPenalty	(	int	hGap,
		int	nGap
	)

Definition at line 38 of file ffScore.c.

References digitsBaseTwo(), and ffIntronMax.

Referenced by ffCalcGapPenalty(), ffCdnaGapPenalty(), and smoothOneGap().

{
int acc = 2;
if (hGap > 400000)      /* Discourage really long introns. */
    {
    acc += (hGap - 400000)/3000;
    if (hGap > ffIntronMax)
        acc += (hGap - ffIntronMax)/2000;
    }
if (hGap < 0)   /* Discourage jumping back in haystack. */
    {
    hGap = -8*hGap;
    if (hGap > 48)
        hGap = (hGap*hGap);
    }
if (nGap < 0)   /* Jumping back in needle gets rid of previous alignment. */
    {
    acc += -nGap;
    nGap = 0;
    }
acc += digitsBaseTwo(hGap)/2;
if (nGap != 0)
    {
    acc += digitsBaseTwo(nGap);
    }
else
    {
    if (hGap > 30)
        acc -= 1;
    }
return acc;
}

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int ffCalcGapPenalty	(	int	hGap,
		int	nGap,
		enum ffStringency	stringency
	)

Definition at line 115 of file ffScore.c.

References calcLooseGap(), calcTightGap(), errAbort(), ffCalcCdnaGapPenalty(), ffCdna, ffLoose, and ffTight.

Referenced by ffGapPenalty(), scoreAli(), ssGapCost(), ssGraphMake(), and trimGapPenalty().

{
switch (stringency)
    {
    case ffCdna:
        return ffCalcCdnaGapPenalty(hGap, nGap);
    case ffTight:
        return calcTightGap(hGap,nGap);
    case ffLoose:
        return calcLooseGap(hGap,nGap);
    default:
        errAbort("Unknown stringency type %d", stringency);
        return 0;
    }
}

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int ffCdnaGapPenalty	(	struct ffAli *	left,
		struct ffAli *	right
	)

Definition at line 133 of file ffScore.c.

References ffCalcCdnaGapPenalty(), ffAli::hEnd, ffAli::hStart, ffAli::left, ffAli::nEnd, ffAli::nStart, and ffAli::right.

Referenced by reconsiderAlignedGaps().

{
int hGap = right->hStart - left->hEnd;
int nGap = right->nStart - left->nEnd;
return ffCalcCdnaGapPenalty(hGap, nGap);
}

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int ffGapPenalty	(	struct ffAli *	left,
		struct ffAli *	right,
		enum ffStringency	stringency
	)

Definition at line 141 of file ffScore.c.

References ffCalcGapPenalty(), ffAli::hEnd, ffAli::hStart, ffAli::left, ffAli::nEnd, ffAli::nStart, and ffAli::right.

Referenced by ffScoreSomeAlis(), and ffScoreSomething().

{
int hGap = right->hStart - left->hEnd;
int nGap = right->nStart - left->nEnd;
return ffCalcGapPenalty(hGap, nGap, stringency);
}

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int ffScore	(	struct ffAli *	ali,
		enum ffStringency	stringency
	)

Definition at line 195 of file ffScore.c.

References FALSE, and ffScoreSomething().

Referenced by cutAtBigIntrons(), ffFindAndScore(), and ffScoreCdna().

{
return ffScoreSomething(ali, stringency, FALSE);
}

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int ffScoreCdna

(

struct ffAli *

ali

)

Definition at line 201 of file ffScore.c.

References ffCdna, and ffScore().

{
return ffScore(ali, ffCdna);
}

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int ffScoreMatch	(	DNA *	a,
		DNA *	b,
		int	size
	)

Definition at line 17 of file ffScore.c.

Referenced by trimFlakyEnds().

{
int i;
int score = 0;
for (i=0; i<size; ++i)
    {
    DNA aa = a[i];
    DNA bb = b[i];
    if (aa == 'n' || bb == 'n')
        continue;
    if (aa == bb)
        ++score;
    else
        score -= 1;
    }
return score;
}

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int ffScoreProtein	(	struct ffAli *	ali,
		enum ffStringency	stringency
	)

Definition at line 208 of file ffScore.c.

References ffScoreSomething(), and TRUE.

{
return ffScoreSomething(ali, stringency, TRUE);
}

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int ffScoreSomeAlis	(	struct ffAli *	ali,
		int	count,
		enum ffStringency	stringency
	)

Definition at line 149 of file ffScore.c.

References dnaScoreMatch(), ffGapPenalty(), ffAli::hEnd, ffAli::hStart, ffAli::nStart, and ffAli::right.

{
int score = 0;
int oneScore;

while (--count >= 0)
    {
    int len = ali->hEnd - ali->hStart;
    struct ffAli *right = ali->right;
    oneScore = dnaScoreMatch(ali->hStart, ali->nStart, len);
    score += oneScore;
    if (count > 0)  /* Calculate gap penalty */
        score -= ffGapPenalty(ali, right,stringency);
    ali = right;
    }
return score;
}

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int ffScoreSomething	(	struct ffAli *	ali,
		enum ffStringency	stringency,
		boolean	isProt
	)

Definition at line 168 of file ffScore.c.

References aaScoreMatch(), dnaScoreMatch(), ffGapPenalty(), ffAli::hEnd, ffAli::hStart, ffAli::left, ffAli::nStart, and ffAli::right.

Referenced by ffScore(), and ffScoreProtein().

{
int score = 0;
int oneScore;
int (*scoreMatch)(char *a, char *b, int size);

if (ali == NULL)
    return -0x7FFFFFFF;
scoreMatch = (isProt ? aaScoreMatch : dnaScoreMatch );
while (ali->left != NULL) ali = ali->left;
while (ali != NULL)
    {
    int len = ali->hEnd - ali->hStart;
    struct ffAli *right = ali->right;
    oneScore = scoreMatch(ali->hStart, ali->nStart, len);
    score += oneScore;
    if (right)  /* Calculate gap penalty */
        {
        score -= ffGapPenalty(ali, right, stringency);
        }
    ali = right;
    }
return score;
}

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void setFfIntronMax

(

int

value

)

Definition at line 12 of file ffScore.c.

References ffIntronMax.

Referenced by main().

{
ffIntronMax = value;
}

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Variable Documentation

int ffIntronMax = ffIntronMaxDefault

Definition at line 10 of file ffScore.c.

Referenced by ffCalcCdnaGapPenalty(), ffSeedExtInMem(), gfAlignSomeClumps(), gfAlignStrand(), gfAlignTrans(), gfAlignTransTrans(), gfFindAlignAaTrans(), scanIndexForSmallExons(), seedResolvePower(), setFfIntronMax(), and ssStitch().

char const rcsid[] = "$Id: ffScore.c,v 1.5 2003/10/21 22:06:32 kent Exp $" [static]

Definition at line 8 of file ffScore.c.

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