Package org.biojava.bio.structure.align.util

Class Summary

AFPAlignmentDisplay
AFPChainScorer
AlignmentTools	Some utility methods for analyzing and manipulating AFPChains.
AlignmentTools.IdentityMap<K>	A Map can be viewed as a function from K to V.
AtomCache	A utility class that provides easy access to Structure objects.
CacheFactory	provides a SoftHashMap singleton.
CliTools	Utilities for autoconfiguring javabeans based on command line arguments.
CollectionTools	Utilities for working with collections.
HTTPConnectionTools	a class that takes care about opening HttpURLConnections and sets the proper timeouts
ResourceManager	A class that manages the Strings that are defined in the spice.properties file.
SynchronizedOutFile
UserConfiguration	A container to persist config to the file system

Exception Summary

ConfigurationException