Here is a list of all class members with links to the classes they belong to:

- a -

• add() : VectorIntervalMap, TreeIntervalMap, IntervalMap
• AddCopy() : IntervalSeqManipulator
• AluRecord() : AluRecord
• arg_value : MauveOption

- b -

• BbSeqComp() : BbSeqComp
• BbSorter() : BbSorter

- c -

• chainable_groups : NllBuffers
• chained_component_maps : MatchRecord
• chained_matches : MatchRecord
• char1 : aligned_coords_s
• char2 : aligned_coords_s
• clear() : NllBuffers, CompactMatchRecord, MatchRecord, MatchLink
• Clone() : UniqueMatchFinder, SeedMatchEnumerator, TheRealMemHash, GappedMatchRecord, UngappedMatchRecord, CompactUngappedMatchRecord
• CompactMatchRecord() : CompactMatchRecord
• CompactUngappedMatchRecord() : CompactUngappedMatchRecord
• compare() : NeighborhoodGroupComponentCompare
• concat_contig_start : TheRealMemHash
• config_opt : OptionList
• Copy() : GappedMatchRecord, UngappedMatchRecord, CompactUngappedMatchRecord
• CreateMatches() : SeedMatchEnumerator
• CropLeft() : IntervalSeqManipulator
• CropRight() : IntervalSeqManipulator

- d -

• deleted : AluRecord
• distance : NeighborhoodListEntry
• divergent : AluRecord
• dont_extend : MatchRecord

- e -

• end : ProcrastinationQueue, AluRecord
• endDB : AluRecord
• EnumerateMatches() : UniqueMatchFinder, SeedMatchEnumerator
• extended : MatchRecord
• extra_left_subsets : MatchRecord
• extra_right_subsets : MatchRecord

- f -

• finalize() : GappedMatchRecord
• find() : VectorIntervalMap, TreeIntervalMap, IntervalMap
• FindMatches() : SeedMatchEnumerator
• Free() : GappedMatchRecord, UngappedMatchRecord, CompactUngappedMatchRecord

- g -

• GappedMatchRecord() : GappedMatchRecord
• getOptions() : OptionList
• GetSar() : SeedMatchEnumerator
• group_entries : NllBuffers

- h -

• HashMatch() : SeedMatchEnumerator

- i -

• inserted : AluRecord
• IntervalSeqManipulator() : IntervalSeqManipulator
• is_novel_subset : MatchRecord
• iv_map : VectorIntervalMap, TreeIntervalMap

- j -

• j_comp_sort_list : NllBuffers

- l -

• left_subset_links : MatchRecord
• left_superset : MatchRecord
• LeftEnd() : IntervalSeqManipulator
• Length() : IntervalSeqManipulator
• length() : AluRecord
• livComp() : livComp

- m -

• m_seq : livComp, BbSorter, IntervalSeqManipulator, BbSeqComp
• match : NeighborhoodListEntry
• MatchLink() : MatchLink
• MatchRecord() : MatchRecord
• MauveOption() : MauveOption
• max_multiplicity : SeedMatchEnumerator
• mhc : ProcrastinationQueue
• Mi_component : NeighborhoodListEntry
• min_multiplicity : SeedMatchEnumerator
• Mj_component : NeighborhoodListEntry
• MLDeleter() : MLDeleter
• mlist : SeedMatchEnumerator, MLDeleter

- n -

• neighborhood_list : NllBuffers
• NllBuffers() : NllBuffers
• novel_subset_groups : NllBuffers

- o -

• only_direct : SeedMatchEnumerator
• operator()() : TaxonNamePairComparator, PairFirstComparator< PairType >, AlignedCoordSeqIComparator, IntervalCompare, ToUPPER, ProcrastinationQueue::MultiplicityHeapCompare, NeighborhoodGroupCompare, NeighborhoodGroupComponentCompare, NeighborhoodListComparator, IsNullPtr< T >, MatchSortEntryCompare, livComp, TaxonNamePairComparator, ShorterThan, BbSorter, LocComp, AnalRowComp, BbSeqComp
• operator<< : GappedMatchRecord, UngappedMatchRecord
• opt_list : OptionList
• OptionList() : OptionList

- p -

• pop() : ProcrastinationQueue
• pos1 : aligned_coords_s
• pos2 : aligned_coords_s
• prior : AluRecord
• ProcrastinationQueue() : ProcrastinationQueue
• push() : ProcrastinationQueue

- q -

• q : ProcrastinationQueue
• q_end : ProcrastinationQueue
• q_size : ProcrastinationQueue
• queryId : AluRecord

- r -

• relative_orientation : NeighborhoodListEntry
• remaining : AluRecord
• repeatClass : AluRecord
• RepeatHashCat() : TheRealMemHash
• RepeatHashThread() : TheRealMemHash
• repeatId : AluRecord
• right_subset_links : MatchRecord
• right_superset : MatchRecord

- s -

• score : AluRecord
• set : MauveOption
• SetDirection() : SeedMatchEnumerator
• size() : ProcrastinationQueue
• spscore : GappedMatchRecord
• srcc : NeighborhoodGroupCompare
• start : AluRecord
• startDB : AluRecord
• strand : AluRecord
• sub_to_super_map : MatchLink
• subset : MatchLink
• subset_groups : NllBuffers
• subsuming_match : CompactMatchRecord, MatchRecord
• subsumption_component_map : MatchRecord
• super_component_list : MatchLink
• superset : MatchLink
• superset_groups : NllBuffers

- t -

• tandem : MatchRecord

- u -

• UngappedMatchRecord() : UngappedMatchRecord
• UniqueMatchFinder() : UniqueMatchFinder
• usage_info : MauveOption

- ~ -

• ~MLDeleter() : MLDeleter
• ~OptionList() : OptionList
• ~RepeatHashCat() : TheRealMemHash
• ~UniqueMatchFinder() : UniqueMatchFinder

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