| arg_parser | |
| arg_parser::arg_record | |
| CachedESTInfo | A simple class to encapsulate data to be cached about ESTs |
| CLU | CLU: An implementation of the CLU's analysis algorithm, originally developed by Andrey Ptitsyn and Winston Hide |
| CLU::CLUESTData | Container for CLU's hash maps for ESTs |
| ClusterMaker | The base class of all cluster makers |
| ClusterMakerFactory | |
| CmdEntry | A structure to ease delegating processing of commands to various methods in this class |
| D2 | EST Analyzer that uses the D2 algorithm to compute distances between two ESTs |
| D2Zim | EST Analyzer that uses the d2 algorithm to compute distances between two ESTs |
| InteractiveConsole::Entry | |
| EqualInteger | Integer comparison structure for HashMap |
| EqualStr | String comparison structure for HashMap |
| EST | A single EST |
| ESTAnalyzer | The base class of all EST analyzers |
| ESTAnalyzerFactory | |
| ESTCodec | A helper class to serve as a EST enCOder-DECoder |
| ESTCustomData | A dummy class that serves as a place holder |
| Filter | The base class of all filters |
| FilterChain | Class that manages a list of filters |
| FilterFactory | Centralized factory for creating filters |
| FMWSCA | FMWSCA: Framed, Multi-Word String Compare Analyzer |
| FWAnalyzer | FWAnalyzer: Frame and Word based Analyzer |
| GreaterCachedESTInfo | Functor for CachedESTInfo sorting |
| Heuristic | The base class of all heuristics |
| HeuristicChain | Class that manages a list of heuristics |
| HeuristicFactory | |
| InteractiveConsole | An interactive console for manually studying ESTs |
| LCFilter | A filter to weed out reads with Low Complexity (LC) sections |
| LengthFilter | A simple filter to filter out reads shorter than a given length |
| LessCachedESTInfo | Functor for CachedESTInfo sorting |
| EST::LessEST | Functor for EST sorting |
| MatrixFileAnalyzer | MatrixFileAnalyzer: EST Analyzer that simply obtains distances from a matrix file for processing |
| MPIStats | A non-instantiable wrapper class to track MPI-related statistics |
| MST | Class to represent a Minimum Spanning Tree (MST) |
| MSTCache | A cache to maintain similarity/distance metrics to build a Minimum Spanning Tree (MST) |
| MSTCluster | Class to encapsulate cluster information and aid in building clusters using Minimum Spanning Tree (MST) data |
| MSTClusterMaker | A Minimum Spanning Tree (MST) based parallel cluster maker |
| MSTHeapCache | A cache to maintain similarity/distance metrics to build a Minimum Spanning Tree (MST) using a heap |
| MSTMultiListCache | A cache that uses multiple lists to maintain similarity/distance metrics to build a Minimum Spanning Tree (MST) |
| MSTNode | A simple class to represent a MSTNode |
| NewUVHeuristic | Heuristic based upon the "u/v sample heuristic" used in WCD, a type of common word heuristic |
| ESTCodec::NormalEncoder< Shift, Mask > | A functor to generate a encoded word (serves as a hash entry) |
| ParameterSet | Simple class to encapsulate a set of parameters for analyzers and/or heuristics |
| ParameterSetManager | Class that manages a list of parameter sets |
| PartitionData | A simple class to encapsulate data regarding a partition in the PMSTClusterMaker owned by a particular process |
| PMSTClusterMaker | A Minimum Spanning Tree (MST) based parallel cluster maker |
| PMSTHeapCache | A version of the MSTHeapCache that is specialized to work with the Partitioned MST Cluster Maker |
| ResultLog | |
| ESTCodec::RevCompEncoder< Shift, Mask > | A functor to generate a encoded word (serves as a hash entry) |
| TransCacheEntry | Class to encapsulate information needed to apply conditional-transitivity |
| TransMSTClusterMaker | A Minimum Spanning Tree (MST) based parallel cluster maker that uses conditional-transitivity relations to accelerate clustering |
| TVHeuristic | Heuristic based upon the T/V heuristic used in WCD, a type of common word heuristic |
| TwoPassD2 | EST Analyzer that uses the D2 algorithm in both its symmetric and asymmetric variations to compute distance between two ESTs |
| UVSampleHeuristic | Heuristic based upon the "u/v sample heuristic" used in WCD, a type of common word heuristic |
1.6.1