include/nuGappedScoring.h File Reference

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Functions
int4	nuGappedScoring_score (struct ungappedExtension *ungappedExtension, struct PSSMatrix PSSMatrix, int4 subjectSize, unsigned char *subject, int4 dropoff)
void	nuGappedScoring_free ()

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Function Documentation

void nuGappedScoring_free

(

)

Definition at line 956 of file nuGappedScoring.c.

References nuGappedScoring_bestRow, and nuGappedScoring_insertQrow.

Referenced by main().

{
    free(nuGappedScoring_bestRow);
    free(nuGappedScoring_insertQrow);
}

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int4 nuGappedScoring_score	(	struct ungappedExtension *	ungappedExtension,
		struct PSSMatrix	PSSMatrix,
		int4	subjectSize,
		unsigned char *	subject,
		int4	dropoff
	)

Definition at line 26 of file nuGappedScoring.c.

References dpResults::best, dpResults::bestScore, blast_dloc, encoding_extractBase, ungappedExtension::end, int4, PSSMatrix::length, PSSMatrix::matrix, nuGappedScoring_dpAfterSeed(), nuGappedScoring_dpBeforeSeed(), parameters_verboseDloc, PSSMatrix_chop(), coordinate::queryOffset, ungappedExtension::seed, ungappedExtension::start, PSSMatrix::strandLength, and coordinate::subjectOffset.

Referenced by gappedScoring_score().

{
    struct coordinate seed;
    unsigned char *choppedSubject;
    struct PSSMatrix choppedPSSMatrix;
    int4 choppedSubjectSize;
    struct dpResults beforeDpResults, afterDpResults;
    int4 strandOffset = 0;

    seed = ungappedExtension->seed;
//    printf("Seed=%d,%d dloc=%d\n", seed.queryOffset, seed.subjectOffset, blast_dloc);
//      ungappedExtension_print(ungappedExtension); fflush(stdout);

    if (seed.queryOffset > PSSMatrix.strandLength)
    {
            // If query position is in the second strand, remove first strand from PSSM
        strandOffset = PSSMatrix.strandLength;
                seed.queryOffset -= PSSMatrix.strandLength;
                PSSMatrix = PSSMatrix_chop(PSSMatrix, PSSMatrix.strandLength);
    }
    else
    {
        // Otherwise remove second strand
        PSSMatrix.length = PSSMatrix.strandLength;
    }

    // Adjust to point to start of byte
    seed.queryOffset -= 2;
    seed.subjectOffset -= 2;

    // Perform dynamic programming for points before the seed
    beforeDpResults = nuGappedScoring_dpBeforeSeed(subject, PSSMatrix, seed, dropoff);

    // Chop the start off the query and subject so they begin at the seed
    choppedPSSMatrix = PSSMatrix_chop(PSSMatrix, seed.queryOffset);
    choppedSubject = subject + (seed.subjectOffset / 4);
    choppedSubjectSize = subjectSize - seed.subjectOffset;

    // Perform dynamic programming for points after the seed
    afterDpResults = nuGappedScoring_dpAfterSeed(choppedSubject, choppedPSSMatrix,
                                                 dropoff, choppedSubjectSize);

        // Convert best endpoints from bytepacked to unpacked offsets
        afterDpResults.best.subjectOffset *= 4;
        beforeDpResults.best.subjectOffset *= 4;

    // Re-adjust result change due to chopping subject/query and strand adjustment
    afterDpResults.best.queryOffset += seed.queryOffset + strandOffset;
    afterDpResults.best.subjectOffset += seed.subjectOffset;
    beforeDpResults.best.queryOffset += strandOffset;

    // Associate best scoring start and end points with the ungapped extension
    ungappedExtension->start = beforeDpResults.best;
    ungappedExtension->end = afterDpResults.best;

    #ifdef VERBOSE
    if (parameters_verboseDloc == blast_dloc)
        printf("norm[%d,%d,%d](seed=%d,%d)\n", beforeDpResults.bestScore, afterDpResults.bestScore,
                choppedPSSMatrix.matrix[0][encoding_extractBase(choppedSubject[0],seed.subjectOffset % 4)],
            seed.queryOffset, seed.subjectOffset);
        #endif

//      printf("Start=%d,%d End=%d,%d\n", beforeDpResults.best.queryOffset, beforeDpResults.best.subjectOffset,
//                                      afterDpResults.best.queryOffset, afterDpResults.best.subjectOffset);

    // Determine score by combining score from the two traces, and the match score at
    // the seed position
    return beforeDpResults.bestScore + afterDpResults.bestScore +
           choppedPSSMatrix.matrix[0][encoding_extractBase(choppedSubject[0],seed.subjectOffset % 4)];
}

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