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

java.lang.Object
  extended byorg.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
      extended byorg.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(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 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
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.