include/memSingleBlock.h File Reference

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Data Structures
struct	memSingleBlock
Functions
memSingleBlock *	memSingleBlock_initialize (size_t entrySize, int4 blockSize)
void	memSingleBlock_initializeExisting (struct memSingleBlock *memSingleBlock, size_t entrySize, int4 blockSize)
void *	memSingleBlock_newEntry (struct memSingleBlock *memSingleBlock)
void	memSingleBlock_resetCurrent (struct memSingleBlock *memSingleBlock)
void *	memSingleBlock_getCurrent (struct memSingleBlock *memSingleBlock)
void *	memSingleBlock_getEntry (struct memSingleBlock *memSingleBlock, int4 position)
void *	memSingleBlock_getLastEntry (struct memSingleBlock *memSingleBlock)
void	memSingleBlock_free (struct memSingleBlock *memSingleBlock)

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Function Documentation

void memSingleBlock_free

(

struct memSingleBlock *

memSingleBlock

)

Definition at line 138 of file memSingleBlock.c.

References memSingleBlock::block.

Referenced by alignments_free(), cluster_clusterSequences(), cluster_simpleClusterSequences(), cluster_spexClusterSequences(), rsdb_spexClusterSequences(), wordLookupDFA_build(), and wordLookupDFA_calcFrequencyGroups().

{
        // Free the memory block then struct itself
    free(memSingleBlock->block);
    free(memSingleBlock);
}

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void* memSingleBlock_getCurrent

(

struct memSingleBlock *

memSingleBlock

)

[inline]

Definition at line 104 of file memSingleBlock.c.

References memSingleBlock::block, memSingleBlock::currentEntry, memSingleBlock::entrySize, and memSingleBlock::numEntries.

Referenced by alignments_findFinalAlignments(), alignments_free(), alignments_getFinalAlignmentDescriptions(), alignments_getTracebacks(), cluster_clusterSequences(), cluster_processList(), cluster_processSequenceMatches(), cluster_spexClusterSequences(), main(), qPosList_processList(), rsdb_spexClusterSequences(), and rsdb_updateDiagonalMatches().

{
        void* entry;

    // If we have reached the last entry return NULL
    if (memSingleBlock->currentEntry >= memSingleBlock->numEntries)
    {
        return NULL;
    }
        else
    {
        entry = ((char*)(memSingleBlock->block)) +
                         memSingleBlock->currentEntry * memSingleBlock->entrySize;
                memSingleBlock->currentEntry++;
        return entry;
    }
}

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void* memSingleBlock_getEntry	(	struct memSingleBlock *	memSingleBlock,
		int4	position
	)			[inline]

Definition at line 123 of file memSingleBlock.c.

References memSingleBlock::block, and memSingleBlock::entrySize.

Referenced by alignments_findFinalAlignments(), alignments_findTopFinalAlignments(), alignments_getTracebacks(), alignments_isFinalAlignment(), alignments_loadSubjectsIntoMemory(), alignments_printFinalAlignments(), alignments_printGoodAlignments(), print_gappedAlignmentsBrief(), print_gappedAlignmentsFull(), and wordLookupDFA_build().

{
        void* entry;
        entry = ((char*)(memSingleBlock->block)) + position * memSingleBlock->entrySize;
        return entry;
}

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void* memSingleBlock_getLastEntry

(

struct memSingleBlock *

memSingleBlock

)

[inline]

Definition at line 131 of file memSingleBlock.c.

References memSingleBlock::block, memSingleBlock::entrySize, and memSingleBlock::numEntries.

Referenced by alignments_getTracebacks(), and qPosList_processList().

{
        return ((char*)(memSingleBlock->block)) +
            (memSingleBlock->numEntries - 1) * memSingleBlock->entrySize;
}

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struct memSingleBlock* memSingleBlock_initialize	(	size_t	entrySize,
		int4	blockSize
	)			[read]

Definition at line 20 of file memSingleBlock.c.

References global_malloc().

Referenced by alignments_initialize(), cluster_clusterSequences(), cluster_simpleClusterSequences(), cluster_spexClusterSequences(), main(), rsdb_spexClusterSequences(), and wordLookupDFA_build().

{
        struct memSingleBlock* memSingleBlock;

    // Declare memory for first block
    memSingleBlock = (struct memSingleBlock*)global_malloc(sizeof(struct memSingleBlock));

    if (memSingleBlock == NULL)
    {
                fprintf(stderr, "Error allocating memory\n");
                exit(-1);
    }

    memSingleBlock->blockSize = blockSize;
    memSingleBlock->entrySize = entrySize;
        memSingleBlock->numEntries = 0;

    // Declare memory for the block
    memSingleBlock->block = (void*)global_malloc(memSingleBlock->entrySize * memSingleBlock->blockSize);

    if (memSingleBlock->block == NULL)
    {
                fprintf(stderr, "Error allocating memory\n");
                exit(-1);
    }

    return memSingleBlock;
}

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void memSingleBlock_initializeExisting	(	struct memSingleBlock *	memSingleBlock,
		size_t	entrySize,
		int4	blockSize
	)

Definition at line 51 of file memSingleBlock.c.

References memSingleBlock::block, memSingleBlock::blockSize, memSingleBlock::entrySize, global_malloc(), and memSingleBlock::numEntries.

Referenced by cluster_clusterSequences(), cluster_spexClusterSequences(), qPosList_initialize(), and rsdb_spexClusterSequences().

{
    memSingleBlock->blockSize = blockSize;
    memSingleBlock->entrySize = entrySize;
        memSingleBlock->numEntries = 0;

    // Declare memory for the block
    memSingleBlock->block = (void*)global_malloc(memSingleBlock->entrySize * memSingleBlock->blockSize);

    if (memSingleBlock->block == NULL)
    {
                fprintf(stderr, "Error allocating memory\n");
                exit(-1);
    }
}

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void* memSingleBlock_newEntry

(

struct memSingleBlock *

memSingleBlock

)

[inline]

Definition at line 69 of file memSingleBlock.c.

References memSingleBlock::block, memSingleBlock::blockSize, memSingleBlock::entrySize, global_realloc(), and memSingleBlock::numEntries.

Referenced by alignments_addFinalAlignment(), alignments_addGoodAlignment(), cluster_clusterSequences(), cluster_processList(), cluster_simpleClusterSequences(), cluster_spexClusterSequences(), encoding_replaceWildcards(), qPosList_processList(), rsdb_updateDiagonalMatches(), and wordLookupDFA_build().

{
        void* newEntry;

        // Check if we need to increase the block size
        if (memSingleBlock->numEntries >= memSingleBlock->blockSize)
        {
        // Increase the size
        memSingleBlock->blockSize *= 2;

        memSingleBlock->block = (void*)global_realloc(memSingleBlock->block,
                                 memSingleBlock->entrySize * memSingleBlock->blockSize);

        if (memSingleBlock->block == NULL)
        {
            fprintf(stderr, "Error allocating memory\n");
            exit(-1);
        }
    }

    // Use the next available slot in the latest block
    newEntry = ((char*)(memSingleBlock->block)) + memSingleBlock->numEntries * memSingleBlock->entrySize;

    memSingleBlock->numEntries++;

    return newEntry;
}

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void memSingleBlock_resetCurrent

(

struct memSingleBlock *

memSingleBlock

)

[inline]

Definition at line 98 of file memSingleBlock.c.

References memSingleBlock::currentEntry.

Referenced by alignments_findFinalAlignments(), alignments_free(), alignments_getFinalAlignmentDescriptions(), alignments_getTracebacks(), cluster_clusterSequences(), cluster_processList(), cluster_processSequenceMatches(), cluster_spexClusterSequences(), main(), qPosList_processList(), rsdb_spexClusterSequences(), and rsdb_updateDiagonalMatches().

{
        memSingleBlock->currentEntry = 0;
}

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