org.biojava.bio.seq.db.emblcd

Class EmblCDROMRandomAccess

java.lang.Object

org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess

Direct Known Subclasses:

EntryNamRandomAccess

public abstract class EmblCDROMRandomAccess
extends Object

EmblCDROMRandomAccess is an abstract class whose concrete subclasses can perform fast lookups in EMBL CD-ROM format index files. As the format of the records varies between file types, subclasses should implement two methods; readRecord(), which should parse the record into an array of objects and getRecordKey() which should retrieve the the field from the parsed record on which the records were sorted in the index. This is used during the binary search in the findRecord() method.

Implementing readRecord() is easy because it simply means delegating to the supplied RecordParser and calling the appropriate method on it.

Since:

1.2

Author:

Keith James

Field Summary

Fields

Modifier and Type	Field and Description
protected RandomAccessFile	raIndexFile
protected byte[]	recBytes
protected org.biojava.bio.seq.db.emblcd.RecordParser	recParser A recParser for implementing readRecord() specific to each concrete subclass.

Constructor Summary

Constructors

Constructor and Description
EmblCDROMRandomAccess(File indexFile, int headerLength, int recordLength, long recordCount) Creates a new EmblCDROMRandomAccess object.

Method Summary

Methods

Modifier and Type	Method and Description
void	close() close closes the underlying RandomAccessFile.
Object[]	findRecord(String identifier) findRecord performs a binary search within the file for a record specified by an identifier String.
File	getFile() getFile returns the File wrapped.
protected abstract String	getRecordKey(Object[] record) getRecordKey returns the field from the record on which the records were sorted in the index.
protected abstract Object[]	readRecord() readRecord returns an array of objects parsed from a single record.

Methods inherited from class java.lang.Object

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

Field Detail

raIndexFile

protected RandomAccessFile raIndexFile

recParser

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

A recParser for implementing readRecord() specific to each concrete subclass.

recBytes

protected byte[] recBytes

Constructor Detail

EmblCDROMRandomAccess

public EmblCDROMRandomAccess(File indexFile,
                     int headerLength,
                     int recordLength,
                     long recordCount)
                      throws FileNotFoundException

Creates a new EmblCDROMRandomAccess object.

Parameters:

indexFile - a File to wrap.

headerLength - an int (normally 300 bytes).

recordLength - an int indicating the length of a single record.

recordCount - an long indicating the total number of records.

Throws:

FileNotFoundException - if indexFile cannot be found.

Method Detail

getFile

public File getFile()

getFile returns the File wrapped.

Returns:

a File.

findRecord

public Object[] findRecord(String identifier)
                    throws IOException

findRecord performs a binary search within the file for a record specified by an identifier String.

Parameters:

identifier - a String identifier (sequence ID or accession number).

Returns:

an Object [] array containing the record. If there is no such record an empty array is returned.

Throws:

IOException - if an error occurs.

close

public void close()
           throws IOException

close closes the underlying RandomAccessFile.

Throws:

IOException - if an error occurs.

readRecord

protected 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.

getRecordKey

protected abstract String getRecordKey(Object[] record)

getRecordKey returns the field from the record on which the records were sorted in the index. (i.e. sequence ID or accession number).

Returns:

a String.