sgEvolver Class List

Here are the classes, structs, unions and interfaces with brief descriptions:
aligned_coords_sStore a pair of aligned positions and the characters
AlignedCoordSeqIComparator
Alignment
AlignmentEvolver
DeleterBasic 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 >::GisNodeThis 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 >::GisNodeThis class represents nodes of an Gapped Interval Sequence Tree
gnGapSource
gnStringSource
indel_map_s
indel_sRecords the aligned segments flanking an indel
IndelDeleterThe indel deleter samples deletion locations uniformly and deletion lengths from a poisson distribution
IndelInserterThe indel inserter samples insertion locations uniformly and insertion lengths from a poisson distribution
InserterBasic functionality for classes that perform insertion mutations
InverterMutates sequences by performing inversions
LargeHTDeleterThe small Horizontal Transfer (HT) deleter samples deletion locations uniformly and deletion lengths from a bounded uniform distribution
LargeHTInserterThe small horizontal transfer (HT) inserter samples insertion locations uniformly and insertion lengths from a bounded uniform distribution
LCBLeftComparatorCompares left_end coordinate of two LCBs
MutationEvent
MutatorDefines a generic interface for classes that perform mutations on a sequence alignment
NotGap
SmallHTDeleterThe small Horizontal Transfer (HT) deleter samples deletion locations uniformly and deletion lengths from an exponential distribution
SmallHTInserterThe small horizontal transfer (HT) inserter samples insertion locations uniformly and insertion lengths from an exponential distribution
SourceIntervalThis 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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