/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.seq.db.emblcd;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
/**
* 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.
*
* @author Keith James
* @since 1.2
*/
public class EntryNamRandomAccess extends EmblCDROMRandomAccess
{
public EntryNamRandomAccess(File indexFile,
int headerLength,
int recordLength,
long recordCount)
throws FileNotFoundException
{
super(indexFile, headerLength, recordLength, recordCount);
}
/**
* 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.
*
* @return an Object []
array.
*
* @exception IOException if an error occurs.
*/
protected Object [] readRecord() throws IOException
{
int eof = raIndexFile.read(recBytes);
if (eof == -1)
raIndexFile.close();
return recParser.parseEntryNamRecord(recBytes);
}
/**
* getRecordKey
returns the field from the record on
* which the records were sorted in the index. (i.e. sequence ID
* or accession number).
*
* @return a String
.
*/
protected String getRecordKey(Object [] record)
{
return (String) record[0];
}
}