org.biojava3.core.sequence
Class SequenceOptimizationHints

java.lang.Object
  extended by org.biojava3.core.sequence.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

Nested Class Summary
static class SequenceOptimizationHints.SequenceCollection
           
static class SequenceOptimizationHints.SequenceUsage
           
 
Constructor Summary
SequenceOptimizationHints()
           
 
Method Summary
static SequenceOptimizationHints.SequenceCollection getSequenceCollection()
           
static SequenceOptimizationHints.SequenceUsage getSequenceUsage()
           
static void setSequenceCollection(SequenceOptimizationHints.SequenceCollection aSequenceColection)
           
static void setSequenceUsage(SequenceOptimizationHints.SequenceUsage aSequenceUsage)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SequenceOptimizationHints

public SequenceOptimizationHints()
Method Detail

getSequenceUsage

public static SequenceOptimizationHints.SequenceUsage getSequenceUsage()
Returns:
the sequenceUsage

setSequenceUsage

public static void setSequenceUsage(SequenceOptimizationHints.SequenceUsage aSequenceUsage)
Parameters:
aSequenceUsage - the sequenceUsage to set

getSequenceCollection

public static SequenceOptimizationHints.SequenceCollection getSequenceCollection()
Returns:
the sequenceColection

setSequenceCollection

public static void setSequenceCollection(SequenceOptimizationHints.SequenceCollection aSequenceColection)
Parameters:
aSequenceColection - the sequenceColection to set