Package org.biojava.bio.seq.db

Interface Index

  • All Known Implementing Classes:
    SimpleIndex
    public interface Index
    This defines an index entry for an individual sequence within a set of indexed files.
    Author:
    Matthew Pocock

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      File getFile()
      The file to retrieve from.
      String getID()
      The ID of the sequence at this position in this file.
      int getLength()
      The entry can be slurped out of the file by grabbing length bytes from start.
      long getStart()
      Skipping this number of bytes through the file should put the file pointer to the first byte of the sequence.

    • Method Detail

      • getFile

        File getFile()
        The file to retrieve from.
        Returns:
        the File containing this Sequence

      • getStart

        long getStart()
        Skipping this number of bytes through the file should put the file pointer to the first byte of the sequence.
        Returns:
        the offset within the file

      • getLength

        int getLength()
        The entry can be slurped out of the file by grabbing length bytes from start. If the length can't be read from a store then this method should return -1.
        Returns:
        the length in bytes of this indexed entry

      • getID

        String getID()
        The ID of the sequence at this position in this file.
        Returns:
        the ID of the indexed Sequence