| Class | Description |
|---|---|
| AFPAlignmentDisplay | |
| AFPChainScorer | |
| AlignmentTools |
Methods for analyzing and manipulating AFPChains and for
other pairwise alignment utilities.
|
| AlignmentTools.IdentityMap<K> |
A Map
|
| 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.
|
| RotationAxis |
Calculates the rotation axis for an alignment
|
| SynchronizedOutFile | |
| UserConfiguration |
A container to persist config to the file system
|
| Exception | Description |
|---|---|
| ConfigurationException |
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