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