apollo.config
Class SimpleOverlap

java.lang.Object
  apollo.config.SimpleOverlap

All Implemented Interfaces:

OverlapI

public class SimpleOverlap
extends java.lang.Object
implements OverlapI

areOverlapping determines if two SeqFeatureIs overlap using the currently defined gene definition (from Config.getGeneDefinition(). Obviously this method can be called with FeatureSets such as Genes or Transcripts - it should handle such cases. SimpleOverlap is a Singleton - only need one instance. Can then figure if have default overlap (which SimpleOverlap is) with == to singleton. Rename to DefaultOverlap? or SimpleDefaultOverlap?

Constructor Summary

SimpleOverlap()
Private constractor.

Method Summary

boolean	areOverlapping(SeqFeatureI sa, SeqFeatureI sb) The simple overlap checking function.
static SimpleOverlap	getSimpleOverlap()

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleOverlap

public SimpleOverlap()

Private constractor. Singleton access through getSimpleOverlap this cant be a singleton - needs to be able to be used via TiersIO - nned public constructor for introspection

Method Detail

getSimpleOverlap

public static SimpleOverlap getSimpleOverlap()

areOverlapping

public boolean areOverlapping(SeqFeatureI sa,
                              SeqFeatureI sb)

The simple overlap checking function. This descends both SeqFeature trees until have features and compare them.

Specified by:

areOverlapping in interface OverlapI