include/smithWatermanTraceback.h File Reference

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Functions
gappedExtension *	smithWatermanTraceback_build (struct PSSMatrix PSSMatrix, int4 subjectSize, unsigned char *subject, struct coordinate start, struct coordinate end)

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Function Documentation

struct gappedExtension* smithWatermanTraceback_build	(	struct PSSMatrix	PSSMatrix,
		int4	subjectSize,
		unsigned char *	subject,
		struct coordinate	start,
		struct coordinate	end
	)			[read]

Definition at line 25 of file smithWatermanTraceback.c.

References dpResults::best, dpResults::bestScore, global_malloc(), PSSMatrix_chop(), coordinate::queryOffset, trace::queryStart, smithWatermanTraceback_dynamicProgramming(), smithWatermanTraceback_trace(), coordinate::subjectOffset, trace::subjectStart, and gappedExtension::trace.

Referenced by search_nucleotideSsearch(), and search_proteinSsearch().

{
        struct trace trace;
        struct gappedExtension* gappedExtension;
    struct dpResults dpResults;

    // Only perform dynamic programming on region containing high-scoring alignment
        PSSMatrix = PSSMatrix_chop(PSSMatrix, start.queryOffset);
    PSSMatrix.length = end.queryOffset - start.queryOffset + 1;
    subject += start.subjectOffset;
    subjectSize = end.subjectOffset - start.subjectOffset + 1;

    // Perform dynamic programming
    dpResults = smithWatermanTraceback_dynamicProgramming(subject, PSSMatrix, subjectSize);

/*    printf("lengths=%d,%d\n", PSSMatrix.length, subjectSize);
        printf("Start=%d,%d\n", start.queryOffset, start.subjectOffset);
        printf("End=%d,%d\n", end.queryOffset, end.subjectOffset);
    printf("Best=%d,%d Score=%d dloc=%d\n", dpResults.best.queryOffset, dpResults.best.subjectOffset,
                                                dpResults.bestScore);*/

        // Trace back and create the trace which specifies the alignment
        trace = smithWatermanTraceback_trace(dpResults, PSSMatrix.length, PSSMatrix, subject);
        trace.queryStart += start.queryOffset;
        trace.subjectStart += start.subjectOffset;

        // Create gapped extension
        gappedExtension = (struct gappedExtension*)global_malloc(sizeof(struct gappedExtension));
        gappedExtension->trace = trace;
        gappedExtension->next = NULL;

        gappedExtension->queryEnd = dpResults.best.queryOffset + start.queryOffset;
        gappedExtension->subjectEnd = dpResults.best.subjectOffset + start.subjectOffset;
        gappedExtension->nominalScore = dpResults.bestScore;

        return gappedExtension;
}

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