org.biojava.bio.seq.db.emblcd

Class EmblCDROMIndexReader

java.lang.Object

org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader

Direct Known Subclasses:

AcnumHitReader, AcnumTrgReader, DivisionLkpReader, EntryNamIdxReader

public abstract class EmblCDROMIndexReader
extends Object

EmblCDROMIndexReader is an abstract class whose concrete subclasses read EMBL CD-ROM format indices from an underlying InputStream. This format is used by the EMBOSS package for database indexing (see programs dbiblast, dbifasta, dbiflat and dbigcg). Indexing produces four binary files with a simple format:

• division.lkp : master index
• entrynam.idx : sequence ID index
• acnum.trg : accession number index
• acnum.hit : accession number auxiliary index

Internally EMBOSS checks for Big-endian architechtures and switches the byte order to Little-endian. This means trouble if you try to read the file using DataInputStream, but at least the binaries are consistent across architechtures. This class carries out the necessary conversion.

The EMBL CD-ROM format stores the date in 4 bytes. One byte is unused (the first one), leaving one byte for the day, one for the month and one (!) for the year.

For further information see the EMBOSS documentation, or for a full description, the source code of the dbi programs and the Ajax library.

Since:

1.2

Author:

Keith James

Field Summary

Fields

Modifier and Type	Field and Description
protected InputStream	input
protected org.biojava.bio.seq.db.emblcd.RecordParser	recParser
protected StringBuffer	sb

Constructor Summary

Constructors

Constructor and Description
EmblCDROMIndexReader(InputStream input) Creates a new EmblCDROMIndexReader instance.

Method Summary

Methods

Modifier and Type	Method and Description
void	close() close closes the underlying InputStream.
String	readDBDate() readDBDate reads the date from the index header.
String	readDBName() readDBName returns the database name from the index header.
String	readDBRelease() readDBRelease returns the database release from the index header.
long	readFileLength() readFileLength returns the file length in bytes (stored within the file's header by the indexing program).
byte[]	readRawRecord() readRawRecord returns the raw bytes of a single record from the index.
abstract Object[]	readRecord() readRecord returns an array of objects parsed from a single record.
long	readRecordCount() readRecordCount returns the number of records in the file.
int	readRecordLength() readRecordLength returns the record length (bytes).

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

input

protected InputStream input

sb

protected StringBuffer sb

recParser

protected org.biojava.bio.seq.db.emblcd.RecordParser recParser

Constructor Detail

EmblCDROMIndexReader

public EmblCDROMIndexReader(InputStream input)
                     throws IOException

Creates a new EmblCDROMIndexReader instance. A BufferedInputStream is probably the most suitable.

Parameters:

input - an InputStream.

Throws:

IOException - if an error occurs.

Method Detail

readFileLength

public long readFileLength()

readFileLength returns the file length in bytes (stored within the file's header by the indexing program). This may be called more than once as the value is cached.

Returns:

a long.

readRecordCount

public long readRecordCount()

readRecordCount returns the number of records in the file. This may be called more than once as the value is cached.

Returns:

a long.

readRecordLength

public int readRecordLength()

readRecordLength returns the record length (bytes). This may be called more than once as the value is cached.

Returns:

an int.

readDBName

public String readDBName()

readDBName returns the database name from the index header. This may be called more than once as the value is cached.

Returns:

a String.

readDBRelease

public String readDBRelease()

readDBRelease returns the database release from the index header. This may be called more than once as the value is cached.

Returns:

a String.

readDBDate

public String readDBDate()

readDBDate reads the date from the index header. The date is stored in 4 bytes: 0, unused; 1, year; 2, month; 3, day. With a 1 byte year it's not very much use and I'm not sure that the EMBOSS programs set the value correctly anyway.

Returns:

a String.

readRecord

public abstract Object[] readRecord()
                             throws IOException

readRecord returns an array of objects parsed from a single record. Its content will depend on the type of index file. Concrete subclasses must provide an implementation of this method.

Returns:

an Object [] array.

Throws:

IOException - if an error occurs.

readRawRecord

public byte[] readRawRecord()
                     throws IOException

readRawRecord returns the raw bytes of a single record from the index.

Returns:

a byte [] array.

Throws:

IOException - if an error occurs.

close

public void close()
           throws IOException

close closes the underlying InputStream.

Throws:

IOException - if an error occurs.