org.biojavax.bio.db.biosql
Class BioSQLFeatureFilter.Tools

java.lang.Object
  org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Tools

Enclosing interface:

BioSQLFeatureFilter

public static class BioSQLFeatureFilter.Tools
extends java.lang.Object

A class representing some useful stuff you can do with BioSQLFeatureFilters, for instance converting plain FeatureFilters into a their BioSQLFeatureFilter equivalents (where possible).

Constructor Summary

BioSQLFeatureFilter.Tools()

Method Summary

static BioSQLFeatureFilter

convert(FeatureFilter ff) Convert a non-BioSQL FeatureFilter into a BioSQL one.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BioSQLFeatureFilter.Tools

public BioSQLFeatureFilter.Tools()

Method Detail

convert

public static BioSQLFeatureFilter convert(FeatureFilter ff)

Convert a non-BioSQL FeatureFilter into a BioSQL one. We do this by walking through it, converting any ones we recognise into their BioSQLFeatureFilter equivalents. If we don't recognise them, we take special action. For the child of an And, we can just ignore the missing side and replace the And itself with the remaining side. For everything else, the entire FeatureFilter is replaced by BioSQLFeatureFilter.all else we run the risk of missing out potential candidates. The end result is a filter that can be applied to the database to filter out potential candidates for more rigorous selection in-memory by the default filter() method in AbstractRichSequenceDB. Whether or not the filter picks out everything correctly depends entirely on whether it is made up of BioSQLFeatureFilter elements, or can be converted into them.