include/readNcbidb.h File Reference

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Functions
void	readNcbidb_open (char *filename)
unsigned char *	readNcbidb_getSequence (uint4 sequenceNumber, uint4 *length)
unsigned char *	readNcbidb_getDescription (uint4 sequenceNumber, uint4 *length)
Variables
int	readNcbidb_version
int	readNcbidb_alphabetType
uint4	readNcbidb_numberOfSequences
uint4	readNcbidb_longestSequenceLength
uint8	readNcbidb_numberOfLetters

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Function Documentation

unsigned char* readNcbidb_getDescription	(	uint4	sequenceNumber,
		uint4 *	length
	)

Definition at line 219 of file readNcbidb.c.

References global_malloc(), readNcbidb_descriptionOffsets, readNcbidb_numberOfSequences, readNcbidb_phrFile, readNcbidb_phrFilename, readNcbidb_readASN1sequenceLength(), and uint4.

Referenced by main().

{
        unsigned char* description, *newDescription, *descriptionStart;
    uint4 offset, startPos;

    if (sequenceNumber >= readNcbidb_numberOfSequences)
        return NULL;

        *length = readNcbidb_descriptionOffsets[sequenceNumber + 1]
            - readNcbidb_descriptionOffsets[sequenceNumber] - 1;
        offset = readNcbidb_descriptionOffsets[sequenceNumber];

//    printf("offset=%d length=%d\n", offset, *length); fflush(stdout);

    description = (char*)global_malloc((*length) + 1);
    if (fseek(readNcbidb_phrFile, offset, SEEK_SET) == -1 ||
        fread(description, sizeof(char), *length, readNcbidb_phrFile) < *length)
    {
        fprintf(stderr, "%s\n", strerror(errno));
                fprintf(stderr, "Error reading description from %s\n", readNcbidb_phrFilename);
                exit(-1);
    }
    description[*length] = '\0';

        // Read sequence length in ASN.1 format
    descriptionStart = description + 7;
    descriptionStart = readNcbidb_readASN1sequenceLength(descriptionStart, length);

    // Copy description to new buffer
    newDescription = global_malloc((*length) + 1);
    memcpy(newDescription, descriptionStart, (*length) + 1);
    free(description);

    return newDescription;
}

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unsigned char* readNcbidb_getSequence	(	uint4	sequenceNumber,
		uint4 *	length
	)

Definition at line 150 of file readNcbidb.c.

References global_malloc(), readNcbidb_convertCode(), readNcbidb_numberOfSequences, readNcbidb_psqFile, readNcbidb_psqFilename, readNcbidb_sequenceOffsets, and uint4.

Referenced by main().

{
        char* sequence;
    uint4 offset, position = 0;

    if (sequenceNumber >= readNcbidb_numberOfSequences)
        return NULL;

        *length = readNcbidb_sequenceOffsets[sequenceNumber + 1]
            - readNcbidb_sequenceOffsets[sequenceNumber] - 1;
        offset = readNcbidb_sequenceOffsets[sequenceNumber];

    sequence = (char*)global_malloc(*length);
    if (fseek(readNcbidb_psqFile, offset, SEEK_SET) == -1 ||
        fread(sequence, sizeof(char), *length, readNcbidb_psqFile) < *length)
    {
        fprintf(stderr, "%s\n", strerror(errno));
                fprintf(stderr, "Error reading sequence from %s\n", readNcbidb_psqFilename);
                exit(-1);
    }

    while (position < *length)
    {
                sequence[position] = readNcbidb_convertCode(sequence[position]);
        position++;
    }

    return sequence;
}

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void readNcbidb_open

(

char *

filename

)

Definition at line 48 of file readNcbidb.c.

References global_malloc(), readNcbidb_alphabetType, readNcbidb_descriptionOffsets, readNcbidb_longestSequenceLength, readNcbidb_numberOfLetters, readNcbidb_numberOfSequences, readNcbidb_phrFile, readNcbidb_phrFilename, readNcbidb_pinFile, readNcbidb_pinFilename, readNcbidb_psqFile, readNcbidb_psqFilename, readNcbidb_read64Int(), readNcbidb_readInt(), readNcbidb_sequenceOffsets, readNcbidb_version, and uint4.

Referenced by main().

{
    int titleLength, createdLength;
    char* title, *created;
    uint4 sequenceNumber = 0, headerOffset;

    // Open PIN file
    readNcbidb_pinFilename = global_malloc(strlen(filename) + 5);
    sprintf(readNcbidb_pinFilename, "%s.pin", filename);
    if ((readNcbidb_pinFile = fopen(readNcbidb_pinFilename, "r")) == NULL)
        {
                fprintf(stderr, "Error opening file %s for reading\n", readNcbidb_pinFilename);
                exit(-1);
        }

    // Read header information
        readNcbidb_version = readNcbidb_readInt(readNcbidb_pinFile, readNcbidb_pinFilename);
        readNcbidb_alphabetType = !(readNcbidb_readInt(readNcbidb_pinFile, readNcbidb_pinFilename));

    // Read title
        titleLength = readNcbidb_readInt(readNcbidb_pinFile, readNcbidb_pinFilename);
    title = global_malloc(titleLength + 1);
    if (fread(title, sizeof(char), titleLength, readNcbidb_pinFile) < titleLength)
    {
                fprintf(stderr, "Error reading from file %s\n", readNcbidb_pinFilename);
                exit(-1);
    }
    title[titleLength] = '\0';
//      printf("Title = \"%s\"\n", title);

    // Read creation time
        createdLength = readNcbidb_readInt(readNcbidb_pinFile, readNcbidb_pinFilename);
    created = global_malloc(createdLength + 1);
    if (fread(created, sizeof(char), createdLength, readNcbidb_pinFile) < createdLength)
    {
                fprintf(stderr, "Error reading from file %s\n", readNcbidb_pinFilename);
                exit(-1);
    }
    created[createdLength] = '\0';
//      printf("Created = \"%s\"\n", created);

    // Read more header info
    readNcbidb_numberOfSequences = readNcbidb_readInt(readNcbidb_pinFile, readNcbidb_pinFilename);
    readNcbidb_numberOfLetters = readNcbidb_read64Int(readNcbidb_pinFile, readNcbidb_pinFilename);
        readNcbidb_longestSequenceLength = readNcbidb_readInt(readNcbidb_pinFile, readNcbidb_pinFilename);

//    printf("%d,%llu,%d\n", readNcbidb_numberOfSequences, readNcbidb_numberOfLetters, readNcbidb_longestSequenceLength);

    // Read description offsets
    readNcbidb_descriptionOffsets = global_malloc(sizeof(uint4) * (readNcbidb_numberOfSequences + 1));
    sequenceNumber = 0;
    while (sequenceNumber <= readNcbidb_numberOfSequences)
    {
        readNcbidb_descriptionOffsets[sequenceNumber]
                = readNcbidb_readInt(readNcbidb_pinFile, readNcbidb_pinFilename);
        sequenceNumber++;
    }

    // Read sequence offsets
    readNcbidb_sequenceOffsets = global_malloc(sizeof(uint4) * (readNcbidb_numberOfSequences + 1));
    sequenceNumber = 0;
    while (sequenceNumber <= readNcbidb_numberOfSequences)
    {
        readNcbidb_sequenceOffsets[sequenceNumber]
                = readNcbidb_readInt(readNcbidb_pinFile, readNcbidb_pinFilename);

//              printf("[%d]", readNcbidb_sequenceOffsets[sequenceNumber]);
        sequenceNumber++;
    }

    fclose(readNcbidb_pinFile);

        // Open PHR and PSQ files for reading
    readNcbidb_phrFilename = global_malloc(strlen(filename) + 5);
    sprintf(readNcbidb_phrFilename, "%s.phr", filename);
    if ((readNcbidb_phrFile = fopen(readNcbidb_phrFilename, "r")) == NULL)
        {
                fprintf(stderr, "Error opening file %s for reading\n", readNcbidb_phrFilename);
                exit(-1);
        }
    readNcbidb_psqFilename = global_malloc(strlen(filename) + 5);
    sprintf(readNcbidb_psqFilename, "%s.psq", filename);
    if ((readNcbidb_psqFile = fopen(readNcbidb_psqFilename, "r")) == NULL)
        {
                fprintf(stderr, "Error opening file %s for reading\n", readNcbidb_psqFilename);
                exit(-1);
        }
}

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Variable Documentation

int readNcbidb_alphabetType

Definition at line 3 of file readNcbidb.c.

Referenced by main(), and readNcbidb_open().

uint4 readNcbidb_longestSequenceLength

Definition at line 4 of file readNcbidb.c.

Referenced by readNcbidb_open().

uint8 readNcbidb_numberOfLetters

Definition at line 5 of file readNcbidb.c.

Referenced by readNcbidb_open().

uint4 readNcbidb_numberOfSequences

Definition at line 4 of file readNcbidb.c.

Referenced by main(), readNcbidb_getDescription(), readNcbidb_getSequence(), and readNcbidb_open().

int readNcbidb_version

Definition at line 3 of file readNcbidb.c.

Referenced by readNcbidb_open().

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