aligned_coords_s | Store a pair of aligned positions and the characters |

AlignedCoordSeqIComparator | |

Alignment | |

AlignmentEvolver | |

Deleter | Basic functionality for classes that perform deletion mutations |

GappedIntervalSequence< Key, Allocator > | Class implementing an Interval Sequence Tree this is a tree for storing a changing sequence of intervals that was invented one rainy afternoon by Aaron Darling and Michael Rusch |

GappedIntervalSequence< Key, Allocator >::__generic_iterator< is_const > | |

GappedIntervalSequence< Key, Allocator >::GisNode | This class represents nodes of an Gapped Interval Sequence Tree |

GisSplayTree< Key, Allocator > | Class implementing a Gapped Interval Sequence Tree this tree stores a mapping between sequence and gapped sequence coordinates in a potentially changing sequence Important features are that stabbing queries, stabbing insertions, and stabbing deletions are O( log n ) |

GisSplayTree< Key, Allocator >::__generic_iterator< is_const > | |

GisSplayTree< Key, Allocator >::GisNode | This class represents nodes of an Gapped Interval Sequence Tree |

gnGapSource | |

gnStringSource | |

indel_map_s | |

indel_s | Records the aligned segments flanking an indel |

IndelDeleter | The indel deleter samples deletion locations uniformly and deletion lengths from a poisson distribution |

IndelInserter | The indel inserter samples insertion locations uniformly and insertion lengths from a poisson distribution |

Inserter | Basic functionality for classes that perform insertion mutations |

Inverter | Mutates sequences by performing inversions |

LargeHTDeleter | The small Horizontal Transfer (HT) deleter samples deletion locations uniformly and deletion lengths from a bounded uniform distribution |

LargeHTInserter | The small horizontal transfer (HT) inserter samples insertion locations uniformly and insertion lengths from a bounded uniform distribution |

LCBLeftComparator | Compares left_end coordinate of two LCBs |

MutationEvent | |

Mutator | Defines a generic interface for classes that perform mutations on a sequence alignment |

NotGap | |

SmallHTDeleter | The small Horizontal Transfer (HT) deleter samples deletion locations uniformly and deletion lengths from an exponential distribution |

SmallHTInserter | The small horizontal transfer (HT) inserter samples insertion locations uniformly and insertion lengths from an exponential distribution |

SourceInterval | This class describes an interval of a mutated sequence The interval of sequence is either a range of sequence from another source or is a string of gaps The GappedIntervalSequence will be a search tree of these that tracks sequence coordinates through insertions and deletions, allowing fast lookup of ungapped sequence coordinates in a gapped sequence |

Generated on Mon Aug 19 06:00:53 2013 for sgEvolver by 1.3.6