include/smithWatermanScoring.h File Reference

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Functions
dpResults	smithWatermanScoring_score (struct PSSMatrix PSSMatrix, int4 subjectSize, unsigned char *subject)
dpResults	smithWatermanScoring_scoreReverse (struct PSSMatrix PSSMatrix, int4 subjectSize, unsigned char *subject, struct coordinate end)

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Function Documentation

struct dpResults smithWatermanScoring_score	(	struct PSSMatrix	PSSMatrix,
		int4	subjectSize,
		unsigned char *	subject
	)			[read]

Definition at line 21 of file smithWatermanScoring.c.

References dpResults::bestScore, PSSMatrix::length, PSSMatrix_chop(), and smithWatermanScoring_dynamicProgramming().

Referenced by search_nucleotideSsearch(), search_proteinSsearch(), and smithWatermanScoring_scoreReverse().

{
        struct dpResults dpResults, dpResults2;
        struct PSSMatrix choppedPSSMatrix;

    // If there are two strands
    if (PSSMatrix.strandLength != PSSMatrix.length)
    {
        // Perform dynamic programming on first strand
        choppedPSSMatrix = PSSMatrix;
        choppedPSSMatrix.length = PSSMatrix.strandLength;
                dpResults = smithWatermanScoring_dynamicProgramming(subject, choppedPSSMatrix, subjectSize);

        // Perform dynamic programming on second strand
        choppedPSSMatrix = PSSMatrix_chop(PSSMatrix, PSSMatrix.strandLength);
                dpResults2 = smithWatermanScoring_dynamicProgramming(subject, choppedPSSMatrix, subjectSize);
                dpResults2.best.queryOffset += PSSMatrix.strandLength;

        if (dpResults.bestScore > dpResults2.bestScore)
                return dpResults;
        else
        {
//              printf("[%d:%d,%d]", dpResults2.bestScore, dpResults2.best.queryOffset,
//                                 dpResults2.best.subjectOffset);
                return dpResults2;
                }
    }
        else
    {
        // Perform dynamic programming
        dpResults = smithWatermanScoring_dynamicProgramming(subject, PSSMatrix, subjectSize);

//      printf("Best=%d,%d Score=%d dloc=%d\n", dpResults.best.queryOffset, dpResults.best.subjectOffset,
//                                              dpResults.bestScore, blast_dloc); fflush(stdout);

        return dpResults;
        }
}

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struct dpResults smithWatermanScoring_scoreReverse	(	struct PSSMatrix	PSSMatrix,
		int4	subjectSize,
		unsigned char *	subject,
		struct coordinate	end
	)			[read]

Definition at line 63 of file smithWatermanScoring.c.

References dpResults::best, global_malloc(), PSSMatrix_chop(), PSSMatrix_freeCopy(), PSSMatrix_reverse(), coordinate::queryOffset, smithWatermanScoring_score(), coordinate::subjectOffset, and uint4.

Referenced by search_nucleotideSsearch(), and search_proteinSsearch().

{
        unsigned char* reversedSubject;
        uint4 subjectPosition, strandOffset = 0;
    struct PSSMatrix reversedPSSMatrix;
        struct dpResults dpResults;

        end.queryOffset++;
        end.subjectOffset++;
        
    // If alignment is in the second strand
    if (end.queryOffset > PSSMatrix.strandLength)
    {
        // Remove first strand
        strandOffset = PSSMatrix.strandLength;
        end.queryOffset -= PSSMatrix.strandLength;
        PSSMatrix = PSSMatrix_chop(PSSMatrix, PSSMatrix.strandLength);
        }

    // Remove the end of the PSSM not containing the alignment
    PSSMatrix.strandLength = PSSMatrix.length = end.queryOffset;

    // Shorten the subject to region containing the alignment
    subjectSize = end.subjectOffset;

    // Make a reversed copy of the subject region containing the alignment
    reversedSubject = (unsigned char*)global_malloc(sizeof(char) * subjectSize);
        subjectPosition = 0;
    while (subjectPosition < subjectSize)
    {
        reversedSubject[subjectPosition] = subject[subjectSize - subjectPosition - 1];
        subjectPosition++;
    }

    // Reverse the PSSM
    reversedPSSMatrix = PSSMatrix_reverse(PSSMatrix);

    // Perform smith waterman on reversed sequences
        dpResults = smithWatermanScoring_score(reversedPSSMatrix, subjectSize, reversedSubject);

    dpResults.best.queryOffset = PSSMatrix.length - dpResults.best.queryOffset - 1;
    dpResults.best.subjectOffset = subjectSize - dpResults.best.subjectOffset - 1;
        dpResults.best.queryOffset += strandOffset;

    PSSMatrix_freeCopy(reversedPSSMatrix);
    free(reversedSubject);

    return dpResults;
}

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