Class FileProxyDNASequenceCreator

  • All Implemented Interfaces:

    public class FileProxyDNASequenceCreator
    extends Object
    implements SequenceCreatorInterface<NucleotideCompound>
    This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily. This way you can load very large fasta files and store accession id and delay loading the sequence to save memory. The index is the file stream offset so when a DNASequence has a call to getSequence() the SequenceFileProxyLoader will open the file and offset to the index and retrieve the sequence. Same approach can be used for genome sequence data stored in a local fasta file, in a database or via http interface to a remote server
    Scooter Willis