Class 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

      Constructors 
      Constructor Description
      EntryNamRandomAccess​(java.io.File indexFile, int headerLength, int recordLength, long recordCount)  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method 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 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.