include/gappedScoring.h File Reference

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Functions
int4	gappedScoring_score (struct ungappedExtension *ungappedExtension, struct PSSMatrix PSSMatrix, int4 subjectSize, unsigned char *subject, int4 dropoff)
void	gappedScoring_free ()

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Function Documentation

void gappedScoring_free

(

)

Definition at line 909 of file gappedScoring.c.

References gappedScoring_bestRow, and gappedScoring_insertQrow.

Referenced by main().

{
    free(gappedScoring_bestRow);
    free(gappedScoring_insertQrow);
}

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

Definition at line 24 of file gappedScoring.c.

References dpResults::best, dpResults::bestScore, blast_dloc, blast_numGapped, encoding_alphabetType, encoding_nucleotide, ungappedExtension::end, gappedScoring_dpAfterSeed(), gappedScoring_dpBeforeSeed(), int4, PSSMatrix::length, PSSMatrix::matrix, nuGappedScoring_score(), oldGappedScoring_score(), parameters_restrictedInsertionScoring, parameters_verboseDloc, PSSMatrix_chop(), coordinate::queryOffset, ungappedExtension::seed, ungappedExtension::start, PSSMatrix::strandLength, and coordinate::subjectOffset.

Referenced by alignments_checkForJoin(), alignments_findGoodAlignments(), alignments_getTracebacks(), and alignments_regularGappedAlignment().

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

    // Increment counter number of HSP's gapped
        blast_numGapped++;

    if (encoding_alphabetType == encoding_nucleotide)
    {
        // Use nucleotide gapped alignment code
                return nuGappedScoring_score(ungappedExtension, PSSMatrix, subjectSize, subject, dropoff);
        }

    // Use old code if restricted insertion has been disabled
    if (!parameters_restrictedInsertionScoring)
    {
        return oldGappedScoring_score(ungappedExtension, PSSMatrix, subjectSize, subject, dropoff);
    }

    seed = ungappedExtension->seed;
    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;
    }

    // Perform dynamic programming for points before the seed
    beforeDpResults = gappedScoring_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;
    choppedSubjectSize = subjectSize - seed.subjectOffset;

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

    // 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][choppedSubject[0]], seed.queryOffset, seed.subjectOffset);
        #endif

    // 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][choppedSubject[0]];
}

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