include/ungappedExtension.h File Reference

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Defines
#define	ungappedExtension_DELETED   0
#define	ungappedExtension_UNGAPPED   1
#define	ungappedExtension_SEMIGAPPED   2
#define	ungappedExtension_GAPPED   3
#define	ungappedExtension_JOINED   4
Functions
void	ungappedExtension_initialize ()
ungappedExtension *	ungappedExtension_extend (int2 **queryHit, unsigned char *subjectHit, unsigned char *lastHit, struct PSSMatrix PSSMatrix, unsigned char *subject)
ungappedExtension *	ungappedExtension_oneHitExtend (int2 **queryHit, unsigned char *subjectHit, struct PSSMatrix PSSMatrix, unsigned char *subject)
ungappedExtension *	ungappedExtension_nucleotideExtend (int4 queryHitOffset, int4 subjectHitOffset, struct PSSMatrix PSSMatrix, unsigned char *subject, uint4 subjectLength)
void	ungappedExtension_findSeed (struct ungappedExtension *ungappedExtension, struct PSSMatrix PSSMatrix, unsigned char *subject)
void	ungappedExtension_print (struct ungappedExtension *extension)
Variables
unsigned char *	ungappedExtension_subjectEndReached
int4	ungappedExtension_bestScore
memBlocks *	ungappedExtension_extensions

---

Define Documentation

#define ungappedExtension_DELETED   0

Definition at line 10 of file ungappedExtension.h.

Referenced by alignments_checkForJoin(), alignments_findFinalAlignments(), alignments_findGoodAlignments(), alignments_findTopFinalAlignments(), alignments_getTracebacks(), alignments_pruneRegion(), alignments_regularGappedAlignment(), alignments_unpruneRegion(), and unpack_getRegions().

#define ungappedExtension_GAPPED   3

Definition at line 13 of file ungappedExtension.h.

Referenced by alignments_findGoodAlignments(), and alignments_regularGappedAlignment().

#define ungappedExtension_JOINED   4

Definition at line 14 of file ungappedExtension.h.

Referenced by alignments_checkForJoin().

#define ungappedExtension_SEMIGAPPED   2

Definition at line 12 of file ungappedExtension.h.

Referenced by alignments_findGoodAlignments().

#define ungappedExtension_UNGAPPED   1

Definition at line 11 of file ungappedExtension.h.

Referenced by alignments_unpruneRegion(), ungappedExtension_extend(), ungappedExtension_nucleotideExtend(), and ungappedExtension_oneHitExtend().

---

Function Documentation

struct ungappedExtension* ungappedExtension_extend	(	int2 **	queryHit,
		unsigned char *	subjectHit,
		unsigned char *	lastHit,
		struct PSSMatrix	PSSMatrix,
		unsigned char *	subject
	)			[read]

Definition at line 30 of file ungappedExtension.c.

References blast_ungappedNominalTrigger, ungappedExtension::end, int2, int4, PSSMatrix::matrix, memBlocks_newEntry(), ungappedExtension::next, ungappedExtension::nominalScore, coordinate::queryOffset, ungappedExtension::seed, ungappedExtension::start, statistics_ungappedNominalDropoff, ungappedExtension::status, coordinate::subjectOffset, ungappedExtension_bestScore, ungappedExtension_extensions, ungappedExtension_findProteinSeed(), ungappedExtension_subjectEndReached, and ungappedExtension_UNGAPPED.

Referenced by search_protein2hit().

{
        int2 **queryPosition;
        unsigned char *subjectPosition, *subjectStart, *subjectEnd;
        int4 changeSinceBest = 0;
        int4 dropoff, originalDropoff;

    originalDropoff = dropoff = -statistics_ungappedNominalDropoff;
        ungappedExtension_bestScore = 0;

        // Start at queryEnd,subjectEnd (right/last hit position)
        queryPosition = queryHit;
        subjectPosition = subjectStart = subjectHit;

        // Extend the start of the hit backwards until dropoff
        while (changeSinceBest > dropoff)
        {
                changeSinceBest += (*queryPosition)[*subjectPosition];

        // If we have got a positive score
                if (changeSinceBest > 0)
                {
                        // Keep updating best score and resetting change-since-best
                        // whilst we are reading positive scores
                        do
                        {
                                ungappedExtension_bestScore += changeSinceBest;
                                queryPosition--; subjectPosition--;
                                changeSinceBest = (*queryPosition)[*subjectPosition];
                        }
                        while (changeSinceBest > 0);

                        subjectStart = subjectPosition;
                }
                queryPosition--; subjectPosition--;
        }

        // Correct for extra decrement
        subjectStart++;

        // If best start point is right of previous hit which helped trigger this extension
        // then stop now
        if (subjectStart > lastHit)
        {
                ungappedExtension_subjectEndReached = subjectHit;
                return NULL;
        }

        // Starting at right/last hit position again
        queryPosition = queryHit + 1;
    subjectEnd = subjectHit;
        subjectPosition = subjectHit + 1;
    changeSinceBest = 0;

    // May need to alter dropoff so we also dropoff if below zero
    if (-ungappedExtension_bestScore > originalDropoff)
    {
        dropoff = -ungappedExtension_bestScore;
    }

        // Extend end of alignment until dropoff
        while (changeSinceBest > dropoff)
        {
                changeSinceBest += (*queryPosition)[*subjectPosition];

        // If we have got a positive score
                if (changeSinceBest > 0)
                {
                        // Keep updating best score and resetting change-since-best
                        // whilst we are reading positive scores
                        do
                        {
                                ungappedExtension_bestScore += changeSinceBest;
                                queryPosition++; subjectPosition++;
                                changeSinceBest = (*queryPosition)[*subjectPosition];
                        }
                        while (changeSinceBest > 0);

                        subjectEnd = subjectPosition;

                        // Check need for change in dropoff
            if ((dropoff = -ungappedExtension_bestScore) < originalDropoff)
            {
                dropoff = originalDropoff;
            }
        }
                queryPosition++; subjectPosition++;
        }

        // Correct for extra increment
        subjectEnd--;
        ungappedExtension_subjectEndReached = subjectEnd;

    // If extension scored above trigger for gapping, create object and return it
    if (ungappedExtension_bestScore >= blast_ungappedNominalTrigger)
    {
        int4 diagonal;
        struct ungappedExtension* newUngappedExtension;
        newUngappedExtension = memBlocks_newEntry(ungappedExtension_extensions);

        // Calculate diagonal
        diagonal = (subjectHit - subject) - (queryHit - PSSMatrix.matrix);

        // Determine offsets from pointers
        newUngappedExtension->start.subjectOffset = subjectStart - subject;
        newUngappedExtension->end.subjectOffset = subjectEnd - subject;
        newUngappedExtension->start.queryOffset = newUngappedExtension->start.subjectOffset - diagonal;
        newUngappedExtension->end.queryOffset = newUngappedExtension->end.subjectOffset - diagonal;

        // Find the seed point
        newUngappedExtension->seed = ungappedExtension_findProteinSeed(newUngappedExtension, PSSMatrix, subject);
        // Initialize next to null
        newUngappedExtension->next = NULL;
        newUngappedExtension->nominalScore = ungappedExtension_bestScore;
        newUngappedExtension->status = ungappedExtension_UNGAPPED;

        return newUngappedExtension;
    }
    else
    {
        return NULL;
    }
}

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void ungappedExtension_findSeed	(	struct ungappedExtension *	ungappedExtension,
		struct PSSMatrix	PSSMatrix,
		unsigned char *	subject
	)			[inline]

Definition at line 607 of file ungappedExtension.c.

References encoding_alphabetType, encoding_protein, coordinate::queryOffset, ungappedExtension::seed, coordinate::subjectOffset, ungappedExtension_findNucleotideSeed(), and ungappedExtension_findProteinSeed().

Referenced by alignments_findGoodAlignments(), and alignments_unpruneRegion().

{
        // Find seed if not already recorded
        if (ungappedExtension->seed.queryOffset == -1 && ungappedExtension->seed.subjectOffset == -1)
    {
        if (encoding_alphabetType == encoding_protein)
        {
            ungappedExtension->seed
                = ungappedExtension_findProteinSeed(ungappedExtension, PSSMatrix, subject);
        }
        else
        {
            ungappedExtension->seed
                = ungappedExtension_findNucleotideSeed(ungappedExtension, PSSMatrix, subject);
        }
        }
}

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void ungappedExtension_initialize

(

)

Definition at line 20 of file ungappedExtension.c.

References constants_initialAllocUngappedExtensions, memBlocks_initialize(), parameters_matchScore, parameters_wordTableLetters, ungappedExtension_extensions, ungappedExtension_minus3reward, and ungappedExtension_tableMatchesReward.

Referenced by blast_search().

{
        ungappedExtension_extensions = memBlocks_initialize(sizeof(struct ungappedExtension),
                                   constants_initialAllocUngappedExtensions);
        ungappedExtension_minus3reward = parameters_matchScore * -3;
    ungappedExtension_tableMatchesReward = parameters_matchScore * parameters_wordTableLetters;
}

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struct ungappedExtension* ungappedExtension_nucleotideExtend	(	int4	queryHitOffset,
		int4	subjectHitOffset,
		struct PSSMatrix	PSSMatrix,
		unsigned char *	subject,
		uint4	subjectLength
	)			[read]

Definition at line 274 of file ungappedExtension.c.

References blast_dloc, blast_ungappedNominalTrigger, PSSMatrix::bytePackedCodes, encoding_printLetters(), ungappedExtension::end, int4, PSSMatrix::length, memBlocks_newEntry(), ungappedExtension::next, ungappedExtension::nominalScore, parameters_verboseDloc, parameters_wordTableBytes, parameters_wordTableLetters, PSSMatrix_packedLeftMatchScores, PSSMatrix_packedRightMatchScores, PSSMatrix_packedScore, coordinate::queryOffset, ungappedExtension::seed, ungappedExtension::start, statistics_ungappedNominalDropoff, ungappedExtension::status, PSSMatrix::strandLength, coordinate::subjectOffset, ungappedExtension_bestScore, ungappedExtension_extensions, ungappedExtension_minus3reward, ungappedExtension_subjectEndReached, ungappedExtension_tableMatchesReward, and ungappedExtension_UNGAPPED.

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

{
        unsigned char* queryPosition, *minQueryPosition, *maxQueryPosition;
        unsigned char* subjectPosition, *subjectStart, *subjectEnd;
        int4 dropoff, originalDropoff;
    int4 changeSinceBest = 0;
    int4 matchLettersScore;

        originalDropoff = dropoff = -statistics_ungappedNominalDropoff;

    // Start with score for lookup-table nucleotide match that is not aligned
    ungappedExtension_bestScore = ungappedExtension_tableMatchesReward;

    // Determine minimum query position; either start of the query or start of the second strand
    if (queryHitOffset <= PSSMatrix.strandLength)
    {
        if (queryHitOffset < subjectHitOffset * 4)
            minQueryPosition = PSSMatrix.bytePackedCodes;
        else
            minQueryPosition = PSSMatrix.bytePackedCodes + queryHitOffset - subjectHitOffset * 4;
        }
    else
    {
        if (queryHitOffset - PSSMatrix.strandLength < subjectHitOffset * 4)
            minQueryPosition = PSSMatrix.bytePackedCodes + PSSMatrix.strandLength;
        else
            minQueryPosition = PSSMatrix.bytePackedCodes + queryHitOffset - subjectHitOffset * 4;
    }

        // Start left of hit location
        queryPosition = PSSMatrix.bytePackedCodes + queryHitOffset - parameters_wordTableLetters - 4;
        subjectPosition = subjectStart = subject + subjectHitOffset - parameters_wordTableBytes - 1;

    // Consider partial match of first byte before hit
        matchLettersScore = PSSMatrix_packedLeftMatchScores[*queryPosition ^ *subjectPosition];
    ungappedExtension_bestScore += matchLettersScore;
        changeSinceBest = -matchLettersScore;

    // Move back through alignment until start of query or subject, or until dropoff
    while (queryPosition > minQueryPosition)
    {
        // Add score of matching entire bytes
                changeSinceBest += PSSMatrix_packedScore[*queryPosition ^ *subjectPosition];

        #ifdef VERBOSE
        if (parameters_verboseDloc == blast_dloc)
        {
                printf("<%d< ", PSSMatrix_packedScore[*queryPosition ^ *subjectPosition]);
            printf("["); encoding_printLetters(*queryPosition, 4);
            printf(","); encoding_printLetters(*subjectPosition, 4); printf("]\n");
                }
        #endif

        // If we possibly have a new best score
        if (changeSinceBest > ungappedExtension_minus3reward)
        {
            // Get score for matching individual letters in next byte
                queryPosition-=4; subjectPosition--;
                matchLettersScore = PSSMatrix_packedLeftMatchScores[*queryPosition ^ *subjectPosition];

            // If best score
            if (changeSinceBest + matchLettersScore > 0)
            {
                // Mark new best position
                subjectStart = subjectPosition;

                // Update best score and change since best
                ungappedExtension_bestScore += changeSinceBest + matchLettersScore;
                changeSinceBest = -matchLettersScore;

                #ifdef VERBOSE
                if (parameters_verboseDloc == blast_dloc)
                    printf("(Best=%d)\n", ungappedExtension_bestScore);
                #endif
            }
        }
        else
        {
                // Decrease in score, check dropoff
                        if (changeSinceBest < dropoff)
                break;

            queryPosition-=4; subjectPosition--;
        }
    }

    // Determine maximum query position; either end of the query or end of the first strand
    if (queryHitOffset <= PSSMatrix.strandLength)
    {
        if (PSSMatrix.strandLength - queryHitOffset < subjectLength - subjectHitOffset * 4)
            maxQueryPosition = PSSMatrix.bytePackedCodes + PSSMatrix.strandLength - 4;
        else
            maxQueryPosition = PSSMatrix.bytePackedCodes + (subjectLength - subjectHitOffset * 4)
                             + queryHitOffset - 4;
        }
    else
    {
        if (PSSMatrix.length - queryHitOffset < subjectLength - subjectHitOffset * 4)
            maxQueryPosition = PSSMatrix.bytePackedCodes + PSSMatrix.length - 4;
        else
            maxQueryPosition = PSSMatrix.bytePackedCodes + (subjectLength - subjectHitOffset * 4)
                             + queryHitOffset - 4;
    }

    // Starting right of hit position
        queryPosition = PSSMatrix.bytePackedCodes + queryHitOffset;
        subjectPosition = subjectEnd = subject + subjectHitOffset;
        changeSinceBest = 0;

    // May need to alter dropoff so we also dropoff if below zero
    if (-ungappedExtension_bestScore > originalDropoff)
    {
        dropoff = -ungappedExtension_bestScore;
    }

    // Consider partial match of first byte after hit
        matchLettersScore = PSSMatrix_packedRightMatchScores[*queryPosition ^ *subjectPosition];
    ungappedExtension_bestScore += matchLettersScore;
        changeSinceBest = -matchLettersScore;

    // Move forward through alignment until end of query or subject, or until dropoff
    while (queryPosition < maxQueryPosition)
    {
                // Score of matching entire bytes
                changeSinceBest += PSSMatrix_packedScore[*queryPosition ^ *subjectPosition];

        #ifdef VERBOSE
        if (parameters_verboseDloc == blast_dloc)
        {
                printf(">%d> ", PSSMatrix_packedScore[*queryPosition ^ *subjectPosition]);
            printf("["); encoding_printLetters(*queryPosition, 4);
            printf(","); encoding_printLetters(*subjectPosition, 4); printf("]\n");
            printf("changeSinceBest=%d\n", changeSinceBest);
                }
        #endif

        // If we possibly have a new best score
        if (changeSinceBest > ungappedExtension_minus3reward)
        {
            // Get score for matching individual letters in next byte
                queryPosition+=4; subjectPosition++;
                matchLettersScore = PSSMatrix_packedRightMatchScores[*queryPosition ^ *subjectPosition];

            // If best score
            if (changeSinceBest + matchLettersScore > 0)
            {
                // Mark new best position
                subjectEnd = subjectPosition;

                // Update best score and change since best
                ungappedExtension_bestScore += changeSinceBest + matchLettersScore;
                changeSinceBest = -matchLettersScore;

                #ifdef VERBOSE
                if (parameters_verboseDloc == blast_dloc)
                    printf("(Best=%d)\n", ungappedExtension_bestScore);
                #endif
            }
        }
        else
        {
                // Decrease in score, check dropoff
                        if (changeSinceBest < dropoff)
                break;

            queryPosition+=4; subjectPosition++;
        }
    }

    // Record the point we got to extending forwards
    ungappedExtension_subjectEndReached = subjectPosition;

    // If extension scored above trigger for gapping, create object and return it
    if (ungappedExtension_bestScore >= blast_ungappedNominalTrigger)
    {
        int4 diagonal;
        struct ungappedExtension* newUngappedExtension;
        newUngappedExtension = memBlocks_newEntry(ungappedExtension_extensions);

        // Correct for extra decrement
        subjectStart++;
        // Correct for extra increment
        subjectEnd--;

        // Calculate diagonal
        diagonal = subjectHitOffset * 4 - queryHitOffset;

        // Determine offsets from pointers
        newUngappedExtension->start.subjectOffset = (subjectStart - subject) * 4;
        newUngappedExtension->end.subjectOffset = (subjectEnd - subject) * 4;
        newUngappedExtension->start.queryOffset = newUngappedExtension->start.subjectOffset - diagonal;
        newUngappedExtension->end.queryOffset = newUngappedExtension->end.subjectOffset - diagonal;

                newUngappedExtension->seed.queryOffset = -1;
                newUngappedExtension->seed.subjectOffset = -1;

        // Initialize next to null
        newUngappedExtension->next = NULL;
        newUngappedExtension->nominalScore = ungappedExtension_bestScore;
        newUngappedExtension->status = ungappedExtension_UNGAPPED;

        #ifdef VERBOSE
        if (parameters_verboseDloc == blast_dloc)
        {
            printf("Hit=%d,%d\n", queryHitOffset, subjectHitOffset);
            printf("%d,%d - %d,%d\n", newUngappedExtension->start.queryOffset, newUngappedExtension->start.subjectOffset,
                                      newUngappedExtension->end.queryOffset, newUngappedExtension->end.subjectOffset);
                                      fflush(stdout);
            printf("seed=%d,%d\n", newUngappedExtension->seed.queryOffset, newUngappedExtension->seed.subjectOffset);
                }
                #endif

        return newUngappedExtension;
    }
    else
    {
        return NULL;
    }
}

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struct ungappedExtension* ungappedExtension_oneHitExtend	(	int2 **	queryHit,
		unsigned char *	subjectHit,
		struct PSSMatrix	PSSMatrix,
		unsigned char *	subject
	)			[read]

Definition at line 157 of file ungappedExtension.c.

References blast_ungappedNominalTrigger, ungappedExtension::end, int2, int4, PSSMatrix::matrix, memBlocks_newEntry(), ungappedExtension::next, ungappedExtension::nominalScore, coordinate::queryOffset, ungappedExtension::seed, ungappedExtension::start, statistics_ungappedNominalDropoff, ungappedExtension::status, coordinate::subjectOffset, ungappedExtension_bestScore, ungappedExtension_extensions, ungappedExtension_findProteinSeed(), ungappedExtension_subjectEndReached, and ungappedExtension_UNGAPPED.

Referenced by search_protein1hit().

{
        int2** queryPosition;
        unsigned char* subjectPosition, *subjectStart, *subjectEnd;
        int4 changeSinceBest = 0;
        int4 dropoff, originalDropoff;

        originalDropoff = dropoff = -statistics_ungappedNominalDropoff;
    ungappedExtension_bestScore = 0;

        // Start at queryEnd,subjectEnd (right/last hit position)
        queryPosition = queryHit;
        subjectPosition = subjectStart = subjectHit;

        // Extend the start of the hit forwards until dropoff
        while (changeSinceBest > dropoff)
        {
                changeSinceBest += (*queryPosition)[*subjectPosition];
                // If we have got a positive score
                if (changeSinceBest > 0)
                {
                        // Keep updating best score and resetting change-since-best
                        // whilst we are reading positive scores
                        do
                        {
                                ungappedExtension_bestScore += changeSinceBest;
                                queryPosition--; subjectPosition--;
                                changeSinceBest = (*queryPosition)[*subjectPosition];
                        }
                        while (changeSinceBest > 0);

                        subjectStart = subjectPosition;
                }
                queryPosition--; subjectPosition--;
        }

        // Correct for extra decrement
        subjectStart++;

        // Starting at right/last hit position again
        queryPosition = queryHit + 1;
        subjectPosition = subjectEnd = subjectHit + 1;
        changeSinceBest = 0;

    // May need to alter dropoff so we also dropoff if below zero
    if (-ungappedExtension_bestScore > originalDropoff)
    {
        dropoff = -ungappedExtension_bestScore;
    }

        // Extend end of alignment until dropoff
        while (changeSinceBest > dropoff)
        {
                changeSinceBest += (*queryPosition)[*subjectPosition];
                // If we have got a positive score
                if (changeSinceBest > 0)
                {
                        // Keep updating best score and resetting change-since-best
                        // whilst we are reading positive scores
                        do
                        {
                                ungappedExtension_bestScore += changeSinceBest;
                                queryPosition++; subjectPosition++;
                                changeSinceBest = (*queryPosition)[*subjectPosition];
                        }
                        while (changeSinceBest > 0);

                        subjectEnd = subjectPosition;

                        // Check need for change in dropoff
            if ((dropoff = -ungappedExtension_bestScore) < originalDropoff)
            {
                dropoff = originalDropoff;
            }
        }
                queryPosition++; subjectPosition++;
        }

        // Correct for extra increment
        subjectEnd--;

    // Record the point we got to extending forwards
    ungappedExtension_subjectEndReached = subjectPosition;

    // If extension scored above trigger for gapping, create object and return it
    if (ungappedExtension_bestScore >= blast_ungappedNominalTrigger)
    {
        int4 diagonal;
        struct ungappedExtension* newUngappedExtension;
        newUngappedExtension = memBlocks_newEntry(ungappedExtension_extensions);

        // Calculate diagonal
        diagonal = (subjectHit - subject) - (queryHit - PSSMatrix.matrix);

        // Determine offsets from pointers
        newUngappedExtension->start.subjectOffset = subjectStart - subject;
        newUngappedExtension->end.subjectOffset = subjectEnd - subject;
        newUngappedExtension->start.queryOffset = newUngappedExtension->start.subjectOffset - diagonal;
        newUngappedExtension->end.queryOffset = newUngappedExtension->end.subjectOffset - diagonal;

        // Find the seed point
        newUngappedExtension->seed = ungappedExtension_findProteinSeed(newUngappedExtension, PSSMatrix, subject);
        // Initialize next to null
        newUngappedExtension->next = NULL;
        newUngappedExtension->nominalScore = ungappedExtension_bestScore;
        newUngappedExtension->status = ungappedExtension_UNGAPPED;

        return newUngappedExtension;
    }
    else
    {
        return NULL;
    }
}

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void ungappedExtension_print

(

struct ungappedExtension *

extension

)

Definition at line 766 of file ungappedExtension.c.

References ungappedExtension::end, ungappedExtension::nominalScore, coordinate::queryOffset, ungappedExtension::seed, ungappedExtension::start, ungappedExtension::status, and coordinate::subjectOffset.

Referenced by alignments_checkForJoin(), alignments_findFinalAlignments(), alignments_unpruneRegion(), search_nucleotide(), search_nucleotide_largeTable(), and search_nucleotide_longWord().

{
        printf("Ungapped extension %d,%d to %d,%d score=%d status=%d seed=%d,%d\n",
        extension->start.queryOffset, extension->start.subjectOffset,
        extension->end.queryOffset, extension->end.subjectOffset,
        extension->nominalScore, extension->status,
    extension->seed.queryOffset, extension->seed.subjectOffset);
}

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---

Variable Documentation

int4 ungappedExtension_bestScore

Definition at line 6 of file ungappedExtension.h.

Referenced by search_nucleotide(), search_nucleotide_largeTable(), search_nucleotide_longWord(), ungappedExtension_checkHit(), ungappedExtension_extend(), ungappedExtension_nucleotideExtend(), ungappedExtension_oneHitExtend(), and ungappedExtension_simpleScoring().

struct memBlocks* ungappedExtension_extensions

Definition at line 7 of file ungappedExtension.h.

Referenced by alignments_free(), ungappedExtension_extend(), ungappedExtension_initialize(), ungappedExtension_nucleotideExtend(), and ungappedExtension_oneHitExtend().

unsigned char* ungappedExtension_subjectEndReached

Definition at line 5 of file ungappedExtension.h.

Referenced by search_nucleotide(), search_nucleotide_largeTable(), search_nucleotide_longWord(), search_protein1hit(), search_protein2hit(), ungappedExtension_checkHit(), ungappedExtension_extend(), ungappedExtension_nucleotideExtend(), and ungappedExtension_oneHitExtend().

---