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

- _ -

• __generic_iterator() : GisSplayTree< Key, Allocator >::__generic_iterator< is_const >, GappedIntervalSequence< Key, Allocator >::__generic_iterator< is_const >
• __generic_iterator< false > : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• __generic_iterator< true > : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >

- a -

• addInversion() : Alignment
• alignment : Alignment
• Alignment() : Alignment
• AlignmentEvolver() : AlignmentEvolver
• allocator_type : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• applyDeletion() : Alignment
• applyGapInsertion() : Alignment
• applyInsertion() : Alignment
• applyInversions() : Alignment

- b -

• begin() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >

- c -

• char1 : aligned_coords_s
• char2 : aligned_coords_s
• checkLengths() : Alignment
• checkNodeLengths() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• checkNodeSeqLengths() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• checkTree() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• Clone() : gnStringSource, gnGapSource
• Close() : gnStringSource, gnGapSource
• const_iterator : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• const_node_pointer : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• const_pointer : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• const_reference : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• const_reverse_iterator : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• countNodes() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• CropEnd() : SourceInterval
• CropStart() : SourceInterval

- d -

• debug_checking : GisSplayTree< Key, Allocator >
• decrement() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• Deleter() : Deleter
• deleteSubtree() : GappedIntervalSequence< Key, Allocator >
• deleteTree() : GisSplayTree< Key, Allocator >
• difference_type : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• donor : Mutator, Alignment
• donor_table : Mutator

- e -

• empty() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• end() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• end_node : GappedIntervalSequence< Key, Allocator >
• erase() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• evolve() : AlignmentEvolver

- f -

• find() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• find_seqindex() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• first_lcbs : Alignment
• frequency : MutationEvent

- g -

• gap : SourceInterval
• GappedIntervalSequence() : GappedIntervalSequence< Key, Allocator >
• getBase() : Alignment
• getColumnIndex() : Alignment
• GetContigID() : gnStringSource, gnGapSource
• GetContigListLength() : gnStringSource, gnGapSource
• GetContigName() : gnStringSource, gnGapSource
• GetContigSeqLength() : gnStringSource, gnGapSource
• getDeletionColumns() : Alignment
• GetFilter() : gnStringSource, gnGapSource
• GetLength() : SourceInterval
• getLocation() : Inverter, LargeHTDeleter, SmallHTDeleter, IndelDeleter, Deleter, LargeHTInserter, SmallHTInserter, IndelInserter, Inserter
• GetOpenString() : gnStringSource, gnGapSource
• GetSeqLength() : SourceInterval
• getSequenceStart() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• GetSpec() : gnStringSource, gnGapSource
• getStart() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• gis_tree : GappedIntervalSequence< Key, Allocator >::GisNode
• GisNode() : GisSplayTree< Key, Allocator >::GisNode, GappedIntervalSequence< Key, Allocator >::GisNode
• GisSplayTree() : GisSplayTree< Key, Allocator >
• gnGapSource() : gnGapSource
• gnStringSource() : gnStringSource

- h -

• HasContig() : gnStringSource, gnGapSource

- i -

• increment() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• IndelDeleter() : IndelDeleter
• IndelInserter() : IndelInserter
• insert() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• Inserter() : Inserter
• intervals : Alignment
• inversion_list : Alignment
• Inverter() : Inverter
• isEndNode() : GappedIntervalSequence< Key, Allocator >
• isGap() : SourceInterval
• iterator : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• iterator_category : GisSplayTree< Key, Allocator >::__generic_iterator< is_const >, GappedIntervalSequence< Key, Allocator >::__generic_iterator< is_const >

- k -

• key : GisSplayTree< Key, Allocator >::GisNode, GappedIntervalSequence< Key, Allocator >::GisNode

- l -

• LargeHTDeleter() : LargeHTDeleter
• LargeHTInserter() : LargeHTInserter
• lcb_list : Alignment
• LCBLeftComparator() : LCBLeftComparator
• left : GisSplayTree< Key, Allocator >::GisNode, GappedIntervalSequence< Key, Allocator >::GisNode
• left_block_left : indel_s
• left_block_right : indel_s
• left_end : SourceInterval
• leftEnd() : SourceInterval
• leftmost : GappedIntervalSequence< Key, Allocator >
• length : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >, Alignment, GisSplayTree< Key, Allocator >::GisNode, GappedIntervalSequence< Key, Allocator >::GisNode, SourceInterval

- m -

• m_pFilter : gnStringSource
• m_seq : LCBLeftComparator
• m_spec : gnStringSource, gnGapSource
• max_size : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >, LargeHTDeleter, LargeHTInserter
• min_size : LargeHTDeleter, LargeHTInserter
• mut_events : AlignmentEvolver
• mutate() : Inverter, Deleter, Inserter, Mutator
• MutationEvent() : MutationEvent
• mutator : MutationEvent
• Mutator() : Mutator

- n -

• name : MutationEvent
• node_allocator_type : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• node_pointer : GisSplayTree< Key, Allocator >::__generic_iterator< is_const >, GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >::__generic_iterator< is_const >, GappedIntervalSequence< Key, Allocator >
• nodeCount() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >

- o -

• Open() : gnStringSource, gnGapSource
• operator *() : GisSplayTree< Key, Allocator >::__generic_iterator< is_const >, GappedIntervalSequence< Key, Allocator >::__generic_iterator< is_const >
• operator!= : GisSplayTree< Key, Allocator >::__generic_iterator< is_const >, GappedIntervalSequence< Key, Allocator >::__generic_iterator< is_const >
• operator()() : AlignedCoordSeqIComparator, LCBLeftComparator, NotGap
• operator++() : GisSplayTree< Key, Allocator >::__generic_iterator< is_const >, GappedIntervalSequence< Key, Allocator >::__generic_iterator< is_const >
• operator--() : GisSplayTree< Key, Allocator >::__generic_iterator< is_const >, GappedIntervalSequence< Key, Allocator >::__generic_iterator< is_const >
• operator->() : GisSplayTree< Key, Allocator >::__generic_iterator< is_const >, GappedIntervalSequence< Key, Allocator >::__generic_iterator< is_const >
• operator=() : MutationEvent, Inverter, LargeHTDeleter, SmallHTDeleter, IndelDeleter, LargeHTInserter, SmallHTInserter, IndelInserter, gnStringSource, gnGapSource, GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >, Alignment
• operator== : GisSplayTree< Key, Allocator >::__generic_iterator< is_const >, GappedIntervalSequence< Key, Allocator >::__generic_iterator< is_const >

- p -

• parent : GisSplayTree< Key, Allocator >::GisNode, GappedIntervalSequence< Key, Allocator >::GisNode
• pointer : GisSplayTree< Key, Allocator >::__generic_iterator< is_const >, GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >::__generic_iterator< is_const >, GappedIntervalSequence< Key, Allocator >
• pos1 : aligned_coords_s
• pos2 : aligned_coords_s
• propogateChanges() : GappedIntervalSequence< Key, Allocator >
• ptr_ : GisSplayTree< Key, Allocator >::__generic_iterator< is_const >, GappedIntervalSequence< Key, Allocator >::__generic_iterator< is_const >

- r -

• rbegin() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• Read() : gnStringSource, gnGapSource
• recalculateLengths() : GisSplayTree< Key, Allocator >
• recursiveDelete() : Deleter
• recursiveFind() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• recursiveGetSequenceStart() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• recursiveGetStart() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• recursiveInsert() : Inserter
• recursiveInvert() : Inverter
• recursiveSeqFind() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• reference : GisSplayTree< Key, Allocator >::__generic_iterator< is_const >, GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >::__generic_iterator< is_const >, GappedIntervalSequence< Key, Allocator >
• rend() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• reverse_iterator : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• right : GisSplayTree< Key, Allocator >::GisNode, GappedIntervalSequence< Key, Allocator >::GisNode
• right_block_left : indel_s
• right_block_right : indel_s
• rightmost : GappedIntervalSequence< Key, Allocator >
• root : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >

- s -

• s1_l : indel_map_s
• s1_r : indel_map_s
• s2_l : indel_map_s
• s2_r : indel_map_s
• seq_length : GisSplayTree< Key, Allocator >::GisNode, GappedIntervalSequence< Key, Allocator >::GisNode
• SeqRead() : gnStringSource, gnGapSource
• sequenceLength() : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >, Alignment
• SetFilter() : gnStringSource, gnGapSource
• size : Inverter, SmallHTDeleter, IndelDeleter, SmallHTInserter, IndelInserter
• size_type : GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >
• SmallHTDeleter() : SmallHTDeleter
• SmallHTInserter() : SmallHTInserter
• source_id : SourceInterval
• source_str : gnStringSource
• sourceID() : SourceInterval
• SourceInterval() : SourceInterval
• splay() : GisSplayTree< Key, Allocator >
• subtree_leaves : GappedIntervalSequence< Key, Allocator >::GisNode

- u -

• ungapped_seqs : Alignment

- v -

• value_type : GisSplayTree< Key, Allocator >::__generic_iterator< is_const >, GisSplayTree< Key, Allocator >, GappedIntervalSequence< Key, Allocator >::__generic_iterator< is_const >, GappedIntervalSequence< Key, Allocator >

- w -

• writeAlignment() : Alignment
• writeEvolvedSequences() : Alignment

- ~ -

• ~GappedIntervalSequence() : GappedIntervalSequence< Key, Allocator >
• ~GisSplayTree() : GisSplayTree< Key, Allocator >
• ~gnGapSource() : gnGapSource
• ~gnStringSource() : gnStringSource
• ~LCBLeftComparator() : LCBLeftComparator
• ~Mutator() : Mutator

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