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

EntryNamRandomAccess(File indexFile, int headerLength, int recordLength, long recordCount)

Method Summary

protected String	getRecordKey(Object[] record) getRecordKey returns the field from the record on which the records were sorted in the index.
protected 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(File indexFile,
                            int headerLength,
                            int recordLength,
                            long recordCount)
                     throws FileNotFoundException

Throws:

FileNotFoundException

Method Detail

readRecord

protected Object[] readRecord()
                       throws 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:

IOException - if an error occurs.

getRecordKey

protected 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).

Specified by:

getRecordKey in class EmblCDROMRandomAccess

Returns:

a String.