include/readdb.h File Reference

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Functions
void	readdb_open (char *filename)
int	readdb_readSequence (unsigned char **sequence, uint4 *sequenceLength, uint4 *descriptionStart, uint4 *descriptionLength, uint4 *encodedLength)
int	readdb_nextVolume ()
child *	readdb_getChildren (unsigned char *sequence, uint4 sequenceLength, uint4 encodedLength, uint4 descriptionLocation, uint4 *numChildren)
void	readdb_close ()
Variables
uint4	readdb_numberOfSequences
uint4	readdb_longestSequenceLength
uint4	readdb_dbAlphabetType
uint8	readdb_numberOfLetters
unsigned char *	readdb_filename
unsigned char *	readdb_sequences
uint4	readdb_fileSize
uint4	readdb_sequenceCount
uint4	readdb_descriptionStart
uint4	readdb_volumeNumber
uint4	readdb_numberOfClusters
uint4	readdb_numberOfVolumes
uint4	readdb_numVolumeSequences
uint4	readdb_volume
sequenceData *	readdb_sequenceData

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Function Documentation

void readdb_close

(

)

Definition at line 275 of file readdb.c.

References descriptions_close(), readdb_childBuffer, readdb_dataFilename, readdb_descriptionsFilename, readdb_readData, readdb_sequenceData, readdb_sequenceFilename, readdb_sizeChildBuffer, and readFile_close().

Referenced by blast_search(), and main().

{
        free(readdb_sequenceData);
        free(readdb_sequenceFilename);
    free(readdb_descriptionsFilename);
    free(readdb_dataFilename);
    readFile_close(readdb_readSequences);
    readFile_close(readdb_readData);
    descriptions_close();
    free(readdb_childBuffer);
    readdb_childBuffer = NULL;
    readdb_sizeChildBuffer = 0;
}

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struct child* readdb_getChildren	(	unsigned char *	sequence,
		uint4	sequenceLength,
		uint4	encodedLength,
		uint4	descriptionLocation,
		uint4 *	numChildren
	)			[read]

Definition at line 200 of file readdb.c.

References edit::code, child::descriptionLength, child::descriptionLocation, child::edits, encoding_aaStartWildcards, encoding_sentinalCode, global_malloc(), global_realloc(), child::length, child::numEdits, edit::position, readdb_childBuffer, readdb_sizeChildBuffer, child::regionStart, child::sequence, uint4, and vbyte_getVbyte.

Referenced by alignments_expandCluster(), and main().

{
        unsigned char* edits, *editsEnd;
    struct child* child, *children;
    uint4 editNum, position;

    editsEnd = sequence + encodedLength - 1;

        // Advance to start of child information
        edits = sequence + sequenceLength + 1;

    *numChildren = 0;
        while (edits < editsEnd)
    {
        // Increase size of children buffer if required
        if (*numChildren >= readdb_sizeChildBuffer)
        {
                readdb_sizeChildBuffer = (readdb_sizeChildBuffer + 1) * 2;
                readdb_childBuffer = (struct child*)global_realloc(readdb_childBuffer,
                                  sizeof(struct child) * readdb_sizeChildBuffer);
        }

        child = readdb_childBuffer + *numChildren;

        // Read child details
        vbyte_getVbyte(edits, &(child->descriptionLength));
        vbyte_getVbyte(edits, &(child->regionStart));
        vbyte_getVbyte(edits, &(child->length));
        vbyte_getVbyte(edits, &(child->numEdits));

        // Start with copy of parent sequence
        child->sequence = (unsigned char*)global_malloc(child->length + 2);
                child->sequence++;
        memcpy(child->sequence, sequence + child->regionStart, child->length);
 
        // Add sentinal codes to either end
                child->sequence[-1] = encoding_sentinalCode;
                child->sequence[child->length] = encoding_sentinalCode;

        child->edits = (struct edit*)global_malloc(sizeof(struct edit) * child->numEdits);

        // Read edits and update sequence
        position = 0;
        editNum = 0;
        while (editNum < child->numEdits)
        {
                // Locate the next wildcard in the child
                        while (child->sequence[position] < encoding_aaStartWildcards)
                position++;

            // Read position and character
                child->edits[editNum].position = position;
                        child->edits[editNum].code = *edits;
            edits++;

            // Change character in child
                        child->sequence[position] = child->edits[editNum].code;

                editNum++;
        }

        child->descriptionLocation = descriptionLocation;
        descriptionLocation += child->descriptionLength;
        (*numChildren)++;
    }

    // Copy children from buffer into new memory block and return
        children = (struct child*)global_malloc(sizeof(struct child) * *numChildren);
    memcpy(children, readdb_childBuffer, sizeof(struct child) * *numChildren);

    return children;
}

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int readdb_nextVolume

(

)

Definition at line 123 of file readdb.c.

References readFile::address, sequenceData::descriptionLength, sequenceData::descriptionStart, sequenceData::encodedLength, encoding_alphabetType, encoding_protein, readFile::fileSize, readdb_data, readdb_descriptionStart, readdb_filename, readdb_fileSize, readdb_numberOfClusters, readdb_numberOfVolumes, readdb_numVolumeSequences, readdb_sequenceCount, readdb_sequenceData, readdb_sequenceFilename, readdb_sequences, readdb_volume, readFile_close(), readFile_open(), sequenceData::sequence, sequenceData::sequenceLength, uint4, and vbyte_getVbyte.

Referenced by blast_search(), and main().

{
        uint4 encodedLength, sequenceLength, descriptionLength, sequenceCount = 0, offset = 0;

    // Return 0 if no more volumes to read
        readdb_volume++;
    if (readdb_volume >= readdb_numberOfVolumes)
        return 0;

    // Close current volume
    readFile_close(readdb_readSequences);

    // Open next volume
    sprintf(readdb_sequenceFilename, "%s.sequences%d", readdb_filename, readdb_volume);
    readdb_readSequences = readFile_open(readdb_sequenceFilename);
    readdb_sequences = (unsigned char*)readdb_readSequences.address;

    // Get the sequences file size
        readdb_fileSize = readdb_readSequences.fileSize;

    // For each sequence in next volume volume
    offset = 1;
        sequenceCount = 0;
    while (sequenceCount < readdb_numberOfClusters && offset < readdb_fileSize)
    {
        // Read sequence data
        vbyte_getVbyte(readdb_data, &descriptionLength);
        vbyte_getVbyte(readdb_data, &sequenceLength);
        vbyte_getVbyte(readdb_data, &encodedLength);

        readdb_sequenceData[sequenceCount].descriptionLength = descriptionLength;
        readdb_sequenceData[sequenceCount].descriptionStart = readdb_descriptionStart;
        readdb_sequenceData[sequenceCount].sequenceLength = sequenceLength;
        readdb_sequenceData[sequenceCount].encodedLength = encodedLength;

        // Record pointer to sequence
        readdb_sequenceData[sequenceCount].sequence = readdb_sequences + offset;

        // If protein data skip past sentinal byte
        if (encoding_alphabetType == encoding_protein)
            readdb_sequenceData[sequenceCount].sequence++;

        offset += encodedLength;

        readdb_descriptionStart += descriptionLength;

        sequenceCount++;
    }

    readdb_sequenceCount = 0;
    readdb_numVolumeSequences = sequenceCount;

    return 1;
}

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void readdb_open

(

char *

filename

)

Definition at line 22 of file readdb.c.

References readFile::address, constants_databaseVersion, sequenceData::descriptionLength, descriptions_open(), sequenceData::descriptionStart, sequenceData::encodedLength, encoding_protein, readFile::fileSize, global_malloc(), readdb_data, readdb_dataFilename, readdb_dbAlphabetType, readdb_descriptionsFilename, readdb_descriptionStart, readdb_filename, readdb_fileSize, readdb_longestSequenceLength, readdb_numberOfClusters, readdb_numberOfLetters, readdb_numberOfSequences, readdb_numberOfVolumes, readdb_numVolumeSequences, readdb_readData, readdb_sequenceCount, readdb_sequenceData, readdb_sequenceFilename, readdb_sequences, readdb_volume, readdb_volumeNumber, readFile_checkOpen(), readFile_open(), sequenceData::sequence, sequenceData::sequenceLength, uint4, vbyte_get64vbyte(), vbyte_getVbyte, and wildcards_readWildcards().

Referenced by main().

{
        uint4 databaseVersion, encodedLength, sequenceLength, descriptionLength, sequenceCount, offset;
        char* wildcardsFile;

        readdb_filename = filename;
    readdb_sequenceCount = 0;
    readdb_descriptionStart = 0;
    readdb_volumeNumber = 0;
    readdb_volume = 0;

        // Open sequence file for reading, mapping contents to readdb_address
        readdb_sequenceFilename = (char*)global_malloc(strlen(filename) + 15);
        sprintf(readdb_sequenceFilename, "%s.sequences", filename);

    // Report error if .sequences file doesn't exist
    if (!readFile_checkOpen(readdb_sequenceFilename))
    {
        fprintf(stderr, "Error: unable to open file %s for reading\n", readdb_sequenceFilename);
        fprintf(stderr, "Before searching a collection you must to format it ");
        fprintf(stderr, "using FSA-BLAST's formatdb tool which creates .sequences .descriptions and ");
        fprintf(stderr, ".data files for the collection.\n");
        exit(-1);
    }

    readdb_readSequences = readFile_open(readdb_sequenceFilename);
        readdb_sequences = (char*)readdb_readSequences.address;

    // Open descriptions file for reading
    readdb_descriptionsFilename = (char*)global_malloc(strlen(filename) + 15);
        sprintf(readdb_descriptionsFilename, "%s.descriptions", filename);
    descriptions_open(readdb_descriptionsFilename);

        // Open data file for reading
        readdb_dataFilename = (char*)global_malloc(strlen(filename) + 13);
        sprintf(readdb_dataFilename, "%s.data", filename);
        readdb_readData = readFile_open(readdb_dataFilename);
        readdb_data = (char*)readdb_readData.address;

    // Read in a set of wildcards
    wildcardsFile = (char*)global_malloc(strlen(filename) + 13);
        sprintf(wildcardsFile, "%s.wildcards", filename);
    wildcards_readWildcards(wildcardsFile);
    free(wildcardsFile);

    // Get the sequences file size
        readdb_fileSize = readdb_readSequences.fileSize;

        // Read database statistics
    vbyte_getVbyte(readdb_data, &databaseVersion);
    if (databaseVersion != constants_databaseVersion)
    {
        fprintf(stderr, "Error: Invalid formatted database version %d. ", databaseVersion);
        fprintf(stderr, "Current supported version is %d.\n", constants_databaseVersion);
        fprintf(stderr, "Use formatdb tool to reformat database to version %d.\n",
                        constants_databaseVersion);
        exit(-1);
    }
    vbyte_getVbyte(readdb_data, &readdb_numberOfSequences);
    readdb_data = vbyte_get64vbyte(readdb_data, &readdb_numberOfLetters);
    vbyte_getVbyte(readdb_data, &readdb_longestSequenceLength);
    vbyte_getVbyte(readdb_data, &readdb_dbAlphabetType);
    vbyte_getVbyte(readdb_data, &readdb_numberOfClusters);
    vbyte_getVbyte(readdb_data, &readdb_numberOfVolumes);

        readdb_sequenceData = (struct sequenceData*)global_malloc(sizeof(struct sequenceData)
                        * readdb_numberOfClusters);

        // For each sequence in first volume
    offset = 1;
        sequenceCount = 0;
    while (sequenceCount < readdb_numberOfClusters && offset < readdb_fileSize)
    {
        // Read sequence data
        vbyte_getVbyte(readdb_data, &descriptionLength);
        vbyte_getVbyte(readdb_data, &sequenceLength);
        vbyte_getVbyte(readdb_data, &encodedLength);

        readdb_sequenceData[sequenceCount].descriptionLength = descriptionLength;
        readdb_sequenceData[sequenceCount].descriptionStart = readdb_descriptionStart;
        readdb_sequenceData[sequenceCount].sequenceLength = sequenceLength;
        readdb_sequenceData[sequenceCount].encodedLength = encodedLength;

        // Record pointer to sequence
        readdb_sequenceData[sequenceCount].sequence = readdb_sequences + offset;

        // If protein data skip past sentinal byte
        if (readdb_dbAlphabetType == encoding_protein)
            readdb_sequenceData[sequenceCount].sequence++;

        offset += encodedLength;

        readdb_descriptionStart += descriptionLength;

        sequenceCount++;
    }

    readdb_numVolumeSequences = sequenceCount;
}

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int readdb_readSequence	(	unsigned char **	sequence,
		uint4 *	sequenceLength,
		uint4 *	descriptionStart,
		uint4 *	descriptionLength,
		uint4 *	encodedLength
	)

Definition at line 179 of file readdb.c.

References sequenceData::descriptionLength, sequenceData::descriptionStart, sequenceData::encodedLength, readdb_numVolumeSequences, readdb_sequenceCount, readdb_sequenceData, sequenceData::sequence, and sequenceData::sequenceLength.

Referenced by main().

{
        if (readdb_sequenceCount < readdb_numVolumeSequences)
        {
        *descriptionStart = readdb_sequenceData[readdb_sequenceCount].descriptionStart;
                *descriptionLength = readdb_sequenceData[readdb_sequenceCount].descriptionLength;
                *sequenceLength = readdb_sequenceData[readdb_sequenceCount].sequenceLength;
        *encodedLength = readdb_sequenceData[readdb_sequenceCount].encodedLength;
                *sequence = readdb_sequenceData[readdb_sequenceCount].sequence;

                readdb_sequenceCount++;
        return 1;
        }
        else
    {
        return 0;
        }
}

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Variable Documentation

uint4 readdb_dbAlphabetType

Definition at line 10 of file readdb.c.

Referenced by blast_search(), cluster_writeClusters(), main(), readdb_open(), and rsdb_writeClusters().

uint4 readdb_descriptionStart

Definition at line 13 of file readdb.c.

Referenced by readdb_nextVolume(), and readdb_open().

unsigned char* readdb_filename

Definition at line 12 of file readdb.c.

Referenced by readdb_nextVolume(), and readdb_open().

uint4 readdb_fileSize

Definition at line 13 of file readdb.c.

Referenced by readdb_nextVolume(), and readdb_open().

uint4 readdb_longestSequenceLength

Definition at line 10 of file readdb.c.

Referenced by alignments_expandCluster(), blast_search(), cluster_writeClusters(), main(), and readdb_open().

uint4 readdb_numberOfClusters

Definition at line 16 of file readdb.c.

Referenced by main(), readdb_nextVolume(), and readdb_open().

uint8 readdb_numberOfLetters

Definition at line 11 of file readdb.c.

Referenced by blast_search(), main(), and readdb_open().

uint4 readdb_numberOfSequences

Definition at line 10 of file readdb.c.

Referenced by blast_search(), cluster_writeClusters(), main(), print_XMLfooter(), readdb_open(), and rsdb_writeClusters().

uint4 readdb_numberOfVolumes

Definition at line 16 of file readdb.c.

Referenced by blast_search(), main(), readdb_nextVolume(), and readdb_open().

uint4 readdb_numVolumeSequences

Definition at line 18 of file readdb.c.

Referenced by blast_search(), readdb_nextVolume(), readdb_open(), and readdb_readSequence().

uint4 readdb_sequenceCount

Definition at line 13 of file readdb.c.

Referenced by readdb_nextVolume(), readdb_open(), and readdb_readSequence().

struct sequenceData* readdb_sequenceData

Definition at line 19 of file readdb.c.

Referenced by blast_search(), readdb_close(), readdb_nextVolume(), readdb_open(), and readdb_readSequence().

unsigned char * readdb_sequences

Definition at line 12 of file readdb.c.

Referenced by blast_search(), readdb_nextVolume(), and readdb_open().

uint4 readdb_volume

Definition at line 18 of file readdb.c.

Referenced by blast_search(), readdb_nextVolume(), and readdb_open().

uint4 readdb_volumeNumber

Definition at line 16 of file readdb.c.

Referenced by readdb_open().

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