org.biojava.bio.seq.db.emblcd

Class EntryNamRandomAccess

java.lang.Object

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

org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess

public class EntryNamRandomAccess
extends EmblCDROMRandomAccess

EntryNamRandomAccess objects provide random access to records within the "entrynam.idx" file of an EMBL CD-ROM format binary index. Records are retrieved by their sequence ID.

Since:

1.2

Author:

Keith James

Field Summary

Fields inherited from class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess

raIndexFile, recBytes, recParser

Constructor Summary

Constructors

Constructor and Description
EntryNamRandomAccess(java.io.File indexFile, int headerLength, int recordLength, long recordCount)

Method Summary

Methods

Modifier and Type	Method and Description
protected java.lang.String	getRecordKey(java.lang.Object[] record) getRecordKey returns the field from the record on which the records were sorted in the index.
protected java.lang.Object[]	readRecord() readRecord creates an array of Objects from the raw byte array of a single record.

Methods inherited from class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess

close, findRecord, getFile

Methods inherited from class java.lang.Object

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

Constructor Detail

EntryNamRandomAccess

public EntryNamRandomAccess(java.io.File indexFile,
                    int headerLength,
                    int recordLength,
                    long recordCount)
                     throws java.io.FileNotFoundException

Throws:

java.io.FileNotFoundException

Method Detail

readRecord

protected java.lang.Object[] readRecord()
                                 throws java.io.IOException

readRecord creates an array of Objects from the raw byte array of a single record. For this file type the array contains String seqID, Long rPosition, Long sPosition, Integer fileNumber. See EMBOSS documentation for a full description.

Specified by:

readRecord in class EmblCDROMRandomAccess

Returns:

an Object [] array.

Throws:

java.io.IOException - if an error occurs.

getRecordKey

protected java.lang.String getRecordKey(java.lang.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).

Specified by:

getRecordKey in class EmblCDROMRandomAccess

Returns:

a String.