Class SimpleIndex

java.lang.Object
org.biojava.bio.seq.db.SimpleIndex
All Implemented Interfaces:
Index

public class SimpleIndex extends Object implements Index
This is a no-frills implementation of the Index interface.

The file, start and ID are explicitly maintained as immutable properties of the index. This implementation should be appropriate for many indexing schemes. However, some schemes may wish to implement this interface as a wrapper around a simple file offset, or an array index.

Author:
Matthew Pocock
  • Constructor Summary

    Constructors
    Constructor
    Description
    SimpleIndex(File file, long start, int length, String id)
    Build the index using the given file, start and id
  • Method Summary

    Modifier and Type
    Method
    Description
    The file to retrieve from.
    The ID of the sequence at this position in this file.
    int
    The entry can be slurped out of the file by grabbing length bytes from start.
    long
    Skipping this number of bytes through the file should put the file pointer to the first byte of the sequence.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Constructor Details

    • SimpleIndex

      public SimpleIndex(File file, long start, int length, String id)
      Build the index using the given file, start and id
      Parameters:
      file - the File this sequence is in
      start - how many bytes to skip to reach the first byte of the sequence
      length - how many bytes can be pulled out of the file to grab the record
      id - the ID of the sequence
  • Method Details

    • getFile

      public File getFile()
      Description copied from interface: Index
      The file to retrieve from.
      Specified by:
      getFile in interface Index
      Returns:
      the File containing this Sequence
    • getStart

      public long getStart()
      Description copied from interface: Index
      Skipping this number of bytes through the file should put the file pointer to the first byte of the sequence.
      Specified by:
      getStart in interface Index
      Returns:
      the offset within the file
    • getLength

      public int getLength()
      Description copied from interface: Index
      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.
      Specified by:
      getLength in interface Index
      Returns:
      the length in bytes of this indexed entry
    • getID

      public String getID()
      Description copied from interface: Index
      The ID of the sequence at this position in this file.
      Specified by:
      getID in interface Index
      Returns:
      the ID of the indexed Sequence