Package org.biojava.nbio.core.sequence

Class SequenceOptimizationHints

  • public class SequenceOptimizationHints
extends Object
    A static class that provides optimization hints for memory or performance handling of sequence data. If you are working with genomic sequence data and the use case is sub sequence then the sequence proxy loader implementation may do file reads for each sub-sequence request instead of loading everything into memory. If a large collection of protein sequences is being loaded from a fasta file but only a few sequences will be selected then the file loader could create a sequence proxy loader that retains the offset in the file for each sequence and it is loaded when the sequence data is requested. This way you could load a pointer to all sequences but delay loading until the user actually needs the data. The sequence loader could also have an internal sequence management algorithm that goes through and returns sequence data freeing up memory where a future request for sequence data will then be reloaded.
    Author:
    Scooter Willis