include/hitMatrix.h File Reference

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Functions
void	hitMatrix_initialize (int4 queryLength, int4 maximumSubjectLength, unsigned char *startAddress)
void	hitMatrix_reinitialize (int4 queryLength, int4 maximumSubjectLength, unsigned char *startAddress)
void	hitMatrix_free ()
Variables
unsigned char **	hitMatrix_furthest
int4	hitMatrix_queryLength
uint4	hitMatrix_diagonalMask

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Function Documentation

void hitMatrix_free

(

)

Definition at line 101 of file hitMatrix.c.

References encoding_alphabetType, encoding_protein, hitMatrix_furthest, and hitMatrix_queryLength.

Referenced by blast_search().

{
    if (encoding_alphabetType == encoding_protein)
                hitMatrix_furthest -= hitMatrix_queryLength;
        free(hitMatrix_furthest);
}

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void hitMatrix_initialize	(	int4	queryLength,
		int4	maximumSubjectLength,
		unsigned char *	startAddress
	)

Definition at line 13 of file hitMatrix.c.

References encoding_alphabetType, encoding_nucleotide, global_malloc(), hitMatrix_diagonalMask, hitMatrix_furthest, hitMatrix_queryLength, int4, and parameters_wordSize.

Referenced by blast_search().

{
        int4 numDiagonals;
        unsigned char **minOffset, **offset, **maxOffset;

    // Use more memory efficient but slower hit matrix for nucleotide
    if (encoding_alphabetType == encoding_nucleotide)
    {
        // Calculate number of diagonals that will be required during search
        numDiagonals = 1;
        while (numDiagonals < queryLength + parameters_wordSize)
        {
            numDiagonals <<= 1;
        }

        // Construct mask
        hitMatrix_diagonalMask = numDiagonals - 1;

        // Declare memory for diagonal slots
        hitMatrix_furthest = (unsigned char**)global_malloc(sizeof(unsigned char*) * numDiagonals);
        minOffset = hitMatrix_furthest;
        }
    // Use less memory efficient but faster hit matrix for protein
    else
    {
        // Maximum number of diagonals that will be required during search
        numDiagonals = queryLength + maximumSubjectLength - parameters_wordSize + 1;
        minOffset = (unsigned char**)global_malloc(sizeof(unsigned char*) * numDiagonals);

        // Advance array pointer to allow offset values ranging from
        // -queryLength to subjectLength - wordSize
        hitMatrix_furthest = minOffset + queryLength;
    }

        // Record query length
        hitMatrix_queryLength = queryLength;

        // Start from smallest possible offset value and iterate through to largest
        offset = minOffset;
        maxOffset = minOffset + numDiagonals;

        // For each diagonal, reset furthest to address at start of file
        while (offset < maxOffset)
        {
                *offset = startAddress;
                offset++;
        }
}

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void hitMatrix_reinitialize	(	int4	queryLength,
		int4	maximumSubjectLength,
		unsigned char *	startAddress
	)

Definition at line 63 of file hitMatrix.c.

References encoding_alphabetType, encoding_nucleotide, hitMatrix_furthest, int4, and parameters_wordSize.

Referenced by alignments_expandCluster(), and blast_search().

{
        int4 numDiagonals;
        unsigned char **minOffset, **offset, **maxOffset;

    if (encoding_alphabetType == encoding_nucleotide)
    {
        // Calculate number of diagonals that will be required during search
        numDiagonals = 1;
        while (numDiagonals < queryLength + parameters_wordSize)
        {
            numDiagonals <<= 1;
        }

        minOffset = hitMatrix_furthest;
        }
    // Use less memory efficient but faster hit matrix for protein
    else
    {
        // Maximum number of diagonals that will be required during search
        numDiagonals = queryLength + maximumSubjectLength - parameters_wordSize + 1;

        minOffset = hitMatrix_furthest - queryLength;
    }

        // Start from smallest possible offset value and iterate through to largest
        offset = minOffset;
        maxOffset = minOffset + numDiagonals;

        // For each diagonal, reset furthest to address at start of file
        while (offset < maxOffset)
        {
                *offset = startAddress;
                offset++;
        }
}

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Variable Documentation

uint4 hitMatrix_diagonalMask

Definition at line 6 of file hitMatrix.h.

Referenced by hitMatrix_initialize(), search_nucleotide(), search_nucleotide_largeTable(), and search_nucleotide_longWord().

unsigned char** hitMatrix_furthest

Definition at line 4 of file hitMatrix.h.

Referenced by hitMatrix_free(), hitMatrix_initialize(), hitMatrix_reinitialize(), search_nucleotide(), search_nucleotide_largeTable(), search_nucleotide_longWord(), search_protein1hit(), and search_protein2hit().

int4 hitMatrix_queryLength

Definition at line 5 of file hitMatrix.h.

Referenced by hitMatrix_free(), hitMatrix_initialize(), search_nucleotide(), search_nucleotide_largeTable(), and search_nucleotide_longWord().

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