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
Constructor Summary |
EntryNamRandomAccess(java.io.File indexFile,
int headerLength,
int recordLength,
long recordCount)
|
Method Summary |
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 java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
EntryNamRandomAccess
public EntryNamRandomAccess(java.io.File indexFile,
int headerLength,
int recordLength,
long recordCount)
throws java.io.FileNotFoundException
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
.