src/identityAlign.c File Reference

#include "blast.h"

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Defines
#define	maximum(a, b)   ((a > b) ? a : b)
Functions
void	identityAlign_print (int4 bandStart, int4 bandEnd, int4 seqEnd)
int4	identityAlign_score (unsigned char *seq1, int4 length1, unsigned char *seq2, int4 length2, int4 relativeOffset, uint4 targetScore)
void	identityAlign_free ()
Variables
int4 *	identityAlign_bestRow = NULL
int4	identityAlign_rowSizes = 0

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Define Documentation

#define maximum	(	a,
		b		)	((a > b) ? a : b)

Definition at line 14 of file identityAlign.c.

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Function Documentation

void identityAlign_free

(

)

Definition at line 157 of file identityAlign.c.

References identityAlign_bestRow.

Referenced by main().

{
        free(identityAlign_bestRow);
}

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void identityAlign_print	(	int4	bandStart,
		int4	bandEnd,
		int4	seqEnd
	)

Definition at line 137 of file identityAlign.c.

References identityAlign_bestRow, and int4.

{
    int4 count = 0;
//      printf("[%d,%d,%d]", bandStart, bandEnd, seqEnd); fflush(stdout);

    while (count < bandStart)
    {
                printf("    ");
        count++;
    }

    while (count < bandEnd && count < seqEnd)
    {
                printf("%3d ", identityAlign_bestRow[count]);
        count++;
    }

    printf("\n");
}

int4 identityAlign_score	(	unsigned char *	seq1,
		int4	length1,
		unsigned char *	seq2,
		int4	length2,
		int4	relativeOffset,
		uint4	targetScore
	)

Definition at line 22 of file identityAlign.c.

References global_malloc(), identityAlign_bestRow, identityAlign_rowSizes, int4, and maximum.

Referenced by rsdb_score().

{
        unsigned char *position1, *bestPosition1, *end1;
        unsigned char *position2, *bestPosition2, *end2, *bandStart, *bandEnd;
    int4* bestRow;
        int4 oldBest, match, previousOldBest;
        int4 previousBest;
        int4 bestScore = 0, rowsRemaining = length1;

//    printf("lengths=%d,%d\n", length1, length2);

    bandStart = seq2 - relativeOffset - 10;
    bandEnd = seq2 - relativeOffset + 10;

    end1 = seq1 + length1;
    end2 = seq2 + length2;

        // Declare processing rows for storing match, insert-subject and insert-query values
        // If current malloced rows aren't big enough
        if (length2 >= identityAlign_rowSizes)
        {
                // Free existing rows
                free(identityAlign_bestRow);
                // Set size to double current needed length
                identityAlign_rowSizes = length2 + 1;
                // Malloc new rows
                identityAlign_bestRow = (int4*)global_malloc(sizeof(int4) * identityAlign_rowSizes);
        }

        position1 = seq1 - 1;
        position2 = seq2 - 1;

        // Initialize rows
        bestRow = identityAlign_bestRow;

        // -----FIRST ROW-----
        // For each cell in the top row, scanning from left-to-right
        while (position2 < end2)
        {
                // All values are zero
                *bestRow = 0;

                bestRow++; position2++;
        }

        position1++;

        // -----REMAINING ROWS-----
        while (position1 < end1)
        {
        bandStart++;
        bandEnd++;

                position2 = maximum(seq2 - 1, bandStart);
                bestRow = identityAlign_bestRow + (position2 - seq2) + 1;

        if (position2 < end2 && position2 < bandEnd)
        {
            // -----FAR LEFT CELL-----
            // Set zero values
            *bestRow = 0;
            previousOldBest = 0;
            previousBest = 0;
                }

                position2++; bestRow++;

                // -----REMAINING CELLS-----
                while (position2 < end2 && position2 < bandEnd)
                {
                        // Remember old Best value (for cell below this one)
                        oldBest = *bestRow;

                        // Calculate new M value
            if (*position1 == *position2)
                match = previousOldBest + 1;
            else
                match = previousOldBest;

                        previousOldBest = oldBest;

            // Determine the best of M and Ix
            *bestRow = maximum(maximum(match, oldBest), previousBest);

            previousBest = *bestRow;

            // If this is the best-yet scoring cell
            if (match > bestScore)
            {
                // Update best start cell data
                bestScore = match;
            }

            position2++; bestRow++;
                }

        position1++;
                rowsRemaining--;

        if (rowsRemaining + bestScore < targetScore)
        {
//              printf("Stopped remaining %d/%d\n", rowsRemaining, length1);
                return 0;
                }

//        identityAlign_print(bandStart - seq2, bandEnd - seq2, end2 - seq2);
//              if (dloc==72249)
//                      smithWatermanTraceback_print(identityAlign_bestRow, subjectLength);
        }

//    printf("Finished %d\n", bestScore);
        return bestScore;
}

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Variable Documentation

int4* identityAlign_bestRow = NULL

Definition at line 11 of file identityAlign.c.

Referenced by identityAlign_free(), identityAlign_print(), and identityAlign_score().

int4 identityAlign_rowSizes = 0

Definition at line 12 of file identityAlign.c.

Referenced by identityAlign_score().

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