include/tableGappedScoring.h File Reference

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Functions
int4	tableGappedScoring_score (struct ungappedExtension *ungappedExtension, struct PSSMatrix PSSMatrix, int4 subjectSize, unsigned char *packedSubject, int4 dropoff)

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Function Documentation

int4 tableGappedScoring_score	(	struct ungappedExtension *	ungappedExtension,
		struct PSSMatrix	PSSMatrix,
		int4	subjectSize,
		unsigned char *	packedSubject,
		int4	dropoff
	)

Definition at line 34 of file tableGappedScoring.c.

References dpResults::best, dpResults::bestScore, blast_dloc, blast_numSemiGapped, ungappedExtension::end, int4, ungappedExtension::nominalScore, parameters_bytepackDropoffDecrease, parameters_verboseDloc, PSSMatrix_chop(), coordinate::queryOffset, ungappedExtension::seed, ungappedExtension::start, coordinate::subjectOffset, tableGappedScoring_buildTable(), tableGappedScoring_dpAfterSeed(), tableGappedScoring_dpBeforeSeed(), and tableGappedScoring_table.

Referenced by alignments_findGoodAlignments().

{
    struct coordinate seed;
    unsigned char *choppedSubject;
    struct PSSMatrix choppedPSSMatrix;
    int4 choppedSubjectSize, score, packedSubjectSize;
    struct dpResults beforeDpResults, afterDpResults;

    // Increment counter number of HSP's semi-gapped
        blast_numSemiGapped++;

    dropoff -= parameters_bytepackDropoffDecrease;

    // Calculate packed subject size
    packedSubjectSize = (subjectSize + 3) / 4;

    seed = ungappedExtension->seed;

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

    if (tableGappedScoring_table == NULL)
        tableGappedScoring_buildTable();

    // Update the seed to point to byte-packed sequences
        seed.subjectOffset /= 4;

//    printf("Seed=%d,%d\n", seed.queryOffset, seed.subjectOffset); fflush(stdout);

    // Perform dynamic programming for pointsinitialTable before the seed
    beforeDpResults = tableGappedScoring_dpBeforeSeed(packedSubject, PSSMatrix, seed, dropoff);

//    printf("Score=%d\n", beforeDpResults.bestScore);

        // Adjust starting position to point to non-bytepacked subject
        beforeDpResults.best.subjectOffset *= 4;

    // Chop the start off the query and subject so they begin at the seed
    choppedPSSMatrix = PSSMatrix_chop(PSSMatrix, seed.queryOffset - 1);
    choppedSubject = packedSubject + seed.subjectOffset;
    choppedSubjectSize = packedSubjectSize - seed.subjectOffset;

//    printf("[[%d]]", PSSMatrix.queryCodes[0]);
//    encoding_printLetters(PSSMatrix.xorCodes[0], 4);

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

    // Re-adjust result change due to chopping subject/query and byte packing
    afterDpResults.best.queryOffset += seed.queryOffset - 1;
    afterDpResults.best.subjectOffset = (afterDpResults.best.subjectOffset + seed.subjectOffset) * 4;

    // Extend out ends slightly
        beforeDpResults.best.queryOffset -= 2;
        beforeDpResults.best.subjectOffset -= 2;
        afterDpResults.best.queryOffset += 6;
        afterDpResults.best.subjectOffset += 6;

    #ifdef VERBOSE
    if (parameters_verboseDloc == blast_dloc)
        printf("table[%d,%d](seed=%d,%d)\n", beforeDpResults.bestScore, afterDpResults.bestScore,
                                             seed.queryOffset, seed.subjectOffset * 4);
    #endif

    // Determine score by combining score from the two traces, and the match score at
    // the seed position
    score = beforeDpResults.bestScore + afterDpResults.bestScore;

//      printf("Table score=%d/%d\n", score, ungappedExtension->nominalScore);

        // Use ungapped alignment score and endpoints if better
    if (ungappedExtension->nominalScore > score)
    {
        score = ungappedExtension->nominalScore;
        }
    else
    {
        // Associate best scoring start and end points with the ungapped extension
        ungappedExtension->start = beforeDpResults.best;
        ungappedExtension->end = afterDpResults.best;
    }

    return score;
}

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