- a -

• align_type : Weight
• allow_DI : Weight
• allow_ID : Weight
• alpha : BoltzmannWeight
• alternative_alignments : PartitionDriverBase

- b -

• begin : AlignOverlap::AlternativeSegment
• begin_j : PartitionWorkspace::RowInfo
• beta : BoltzmannWeight

- c -

• curr_back : PartitionWorkspace::ForwardBackwardInfo
• curr_for : PartitionWorkspace::ForwardBackwardInfo
• curr_row : PartitionWorkspace::ForwardBackwardInfo

- d -

• D : DynCell< TYPE > , DynCellMoments< TYPE, N >
• driver_name : PartitionDriverBase

- e -

• end_j : PartitionWorkspace::RowInfo
• errMsg : ExceptionBase
• exp_alpha : BoltzmannWeight
• exp_beta : BoltzmannWeight

- f -

• freq1 : Weight
• freq2 : Weight

- g -

• gap_extension : Weight
• gap_open : Weight

- i -

• I : DynCell< TYPE > , DynCellMoments< TYPE, N >
• i : PartitionWorkspace::ForwardBackwardInfo , Pair
• intToLetter : Alphabet
• intToSet : Alphabet

- j -

• j : Pair

- l -

• last_for : PartitionWorkspace::ForwardBackwardInfo
• last_row : PartitionWorkspace::ForwardBackwardInfo
• letterToInt : Alphabet

- m -

• M : DynCell< TYPE > , DynCellMoments< TYPE, N >

- n -

• n_basic_letters : Alphabet
• n_matches : AlignOverlap::AlignSegment
• next_row : PartitionWorkspace::ForwardBackwardInfo

- o -

• overlap : AlignOverlap::AlignSegment

- p -

• pair : AlignEntry
• pos : Align::GapsAlignedError
• posterior : AlignEntry

- s -

• scale : Weight
• start_pos : AlignOverlap::AlignSegment

- t -

• t : OptCell
• temper : BoltzmannWeight

- w -

• ws : PartitionDriverBase