sgEvolver Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

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

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