| AFPAlignmentDisplay |
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| AFPChainScorer |
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| AlignmentTools |
Methods for analyzing and manipulating AFPChains and for
other pairwise alignment utilities.
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| AlignmentTools.IdentityMap<K> |
A Map can be viewed as a function from K to V.
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| AtomCache |
A utility class that provides easy access to Structure objects.
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| CliTools |
Utilities for autoconfiguring javabeans based on command line arguments.
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| CollectionTools |
Utilities for working with collections.
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| ResourceManager |
A class that manages the Strings that are defined in the spice.properties file.
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| RotationAxis |
Calculates the rotation axis for an alignment
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| SynchronizedOutFile |
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| URLConnectionTools |
A class that takes care about opening URLConnections and sets the proper timeouts
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| UserConfiguration |
A container to persist config to the file system
|