List of all items

Structs

• a_star_aligner::alignment_geometry::AlignmentCoordinates
• a_star_aligner::alignment_geometry::AlignmentRange
• a_star_aligner::alignment_result::AlignmentStatistics
• a_star_aligner::alignment_result::a_star_sequences::SequencePair
• a_star_aligner::alignment_result::alignment::Alignment
• a_star_aligner::alignment_result::alignment::iter::CompactAlignmentIter
• a_star_aligner::alignment_result::alignment::iter::CompactAlignmentIterCloned
• a_star_aligner::alignment_result::alignment::iter::FlatAlignmentIter
• a_star_aligner::alignment_result::alignment::iter::FlatAlignmentIterCloned
• a_star_aligner::alignment_result::alignment::iter::NoLengthDecreaser
• a_star_aligner::alignment_result::alignment::iter::PeekBackMultiplicityMut
• a_star_aligner::alignment_result::alignment::iter::PeekFrontMultiplicityMut
• a_star_aligner::alignment_result::alignment::iter::RefMutLengthDecreaser
• a_star_aligner::alignment_result::alignment::stream::AlignmentStream
• a_star_aligner::alignment_result::alignment::stream::AlignmentStreamCoordinates
• a_star_aligner::configurable_a_star_align::Aligner
• a_star_aligner::configurable_a_star_align::alphabets::ascii_alphabet::AlphabetCharacterFromToAsciiTable
• a_star_aligner::configurable_a_star_align::alphabets::ascii_alphabet::AsciiAlphabet
• a_star_aligner::configurable_a_star_align::alphabets::ascii_alphabet::AsciiCharacter
• a_star_aligner::configurable_a_star_align::alphabets::dna_alphabet::AlphabetCharacterFromToAsciiTable
• a_star_aligner::configurable_a_star_align::alphabets::dna_alphabet::DnaAlphabet
• a_star_aligner::configurable_a_star_align::alphabets::dna_alphabet::DnaCharacter
• a_star_aligner::configurable_a_star_align::alphabets::dna_alphabet_or_n::AlphabetCharacterFromToAsciiTable
• a_star_aligner::configurable_a_star_align::alphabets::dna_alphabet_or_n::DnaAlphabetOrN
• a_star_aligner::configurable_a_star_align::alphabets::dna_alphabet_or_n::DnaCharacterOrN
• a_star_aligner::configurable_a_star_align::alphabets::dna_iupac_nucleic_acid_alphabet::AlphabetCharacterFromToAsciiTable
• a_star_aligner::configurable_a_star_align::alphabets::dna_iupac_nucleic_acid_alphabet::DnaIupacNucleicAcidAlphabet
• a_star_aligner::configurable_a_star_align::alphabets::dna_iupac_nucleic_acid_alphabet::DnaIupacNucleicAcidCharacter
• a_star_aligner::configurable_a_star_align::alphabets::famsa_amino_acid_alphabet::AlphabetCharacterFromToAsciiTable
• a_star_aligner::configurable_a_star_align::alphabets::famsa_amino_acid_alphabet::FamsaAminoAcidAlphabet
• a_star_aligner::configurable_a_star_align::alphabets::famsa_amino_acid_alphabet::FamsaAminoAcidCharacter
• a_star_aligner::configurable_a_star_align::alphabets::generic_alphabet::GenericAlphabet
• a_star_aligner::configurable_a_star_align::alphabets::generic_alphabet::GenericCharacter
• a_star_aligner::configurable_a_star_align::alphabets::iupac_amino_acid_alphabet::AlphabetCharacterFromToAsciiTable
• a_star_aligner::configurable_a_star_align::alphabets::iupac_amino_acid_alphabet::IupacAminoAcidAlphabet
• a_star_aligner::configurable_a_star_align::alphabets::iupac_amino_acid_alphabet::IupacAminoAcidCharacter
• a_star_aligner::configurable_a_star_align::alphabets::rna_alphabet::AlphabetCharacterFromToAsciiTable
• a_star_aligner::configurable_a_star_align::alphabets::rna_alphabet::RnaAlphabet
• a_star_aligner::configurable_a_star_align::alphabets::rna_alphabet::RnaCharacter
• a_star_aligner::configurable_a_star_align::alphabets::rna_alphabet_or_n::AlphabetCharacterFromToAsciiTable
• a_star_aligner::configurable_a_star_align::alphabets::rna_alphabet_or_n::RnaAlphabetOrN
• a_star_aligner::configurable_a_star_align::alphabets::rna_alphabet_or_n::RnaCharacterOrN
• a_star_aligner::configurable_a_star_align::alphabets::rna_iupac_nucleic_acid_alphabet::AlphabetCharacterFromToAsciiTable
• a_star_aligner::configurable_a_star_align::alphabets::rna_iupac_nucleic_acid_alphabet::RnaIupacNucleicAcidAlphabet
• a_star_aligner::configurable_a_star_align::alphabets::rna_iupac_nucleic_acid_alphabet::RnaIupacNucleicAcidCharacter
• a_star_aligner::gap_affine_edit_distance::Context
• a_star_aligner::gap_affine_edit_distance::Identifier
• a_star_aligner::gap_affine_edit_distance::Node
• a_star_aligner::gap_affine_edit_distance::ScoringTable
• a_star_aligner::template_switch_distance::EqualCostRange
• a_star_aligner::template_switch_distance::Node
• a_star_aligner::template_switch_distance::NodeData
• a_star_aligner::template_switch_distance::context::Context
• a_star_aligner::template_switch_distance::context::DynamicStrategies
• a_star_aligner::template_switch_distance::context::Memory
• a_star_aligner::template_switch_distance::lower_bounds::template_switch::TSLBMatrixEntry
• a_star_aligner::template_switch_distance::lower_bounds::template_switch::TemplateSwitchLowerBoundMatrix
• a_star_aligner::template_switch_distance::lower_bounds::template_switch_alignment::TemplateSwitchAlignmentLowerBoundMatrix
• a_star_aligner::template_switch_distance::strategies::AlignmentStrategiesNodeMemory
• a_star_aligner::template_switch_distance::strategies::AlignmentStrategySelection
• a_star_aligner::template_switch_distance::strategies::chaining::ChainingMemory
• a_star_aligner::template_switch_distance::strategies::chaining::LowerBoundChainingStrategy
• a_star_aligner::template_switch_distance::strategies::chaining::NoChainingStrategy
• a_star_aligner::template_switch_distance::strategies::chaining::PrecomputeOnlyChainingStrategy
• a_star_aligner::template_switch_distance::strategies::descendant::AnyTemplateSwitchDescendantStrategy
• a_star_aligner::template_switch_distance::strategies::descendant::OnlyEqualTemplateSwitchDescendantStrategy
• a_star_aligner::template_switch_distance::strategies::node_ord::AntiDiagonalNodeOrdStrategy
• a_star_aligner::template_switch_distance::strategies::node_ord::CostOnlyNodeOrdStrategy
• a_star_aligner::template_switch_distance::strategies::primary_match::AllowPrimaryMatchStrategy
• a_star_aligner::template_switch_distance::strategies::primary_match::MaxConsecutivePrimaryMatchMemory
• a_star_aligner::template_switch_distance::strategies::primary_match::MaxConsecutivePrimaryMatchStrategy
• a_star_aligner::template_switch_distance::strategies::primary_range::NoPrunePrimaryRangeStrategy
• a_star_aligner::template_switch_distance::strategies::primary_range::RangePrunePrimaryRangeStrategy
• a_star_aligner::template_switch_distance::strategies::secondary_deletion::AllowSecondaryDeletionStrategy
• a_star_aligner::template_switch_distance::strategies::secondary_deletion::ForbidSecondaryDeletionStrategy
• a_star_aligner::template_switch_distance::strategies::shortcut::NoShortcutStrategy
• a_star_aligner::template_switch_distance::strategies::shortcut::TemplateSwitchLowerBoundShortcutStrategy
• a_star_aligner::template_switch_distance::strategies::template_switch_count::MaxTemplateSwitchCountStrategy
• a_star_aligner::template_switch_distance::strategies::template_switch_count::NoTemplateSwitchCountStrategy
• a_star_aligner::template_switch_distance::strategies::template_switch_min_length::LookaheadMemoryKey
• a_star_aligner::template_switch_distance::strategies::template_switch_min_length::LookaheadTemplateSwitchMinLengthStrategy
• a_star_aligner::template_switch_distance::strategies::template_switch_min_length::NoTemplateSwitchMinLengthStrategy
• a_star_aligner::template_switch_distance::strategies::template_switch_min_length::PreprocessedLookaheadTemplateSwitchMinLengthStrategy
• a_star_aligner::template_switch_distance::strategies::template_switch_min_length::PreprocessedTemplateSwitchMinLengthStrategy
• a_star_aligner::template_switch_distance::strategies::template_switch_total_length::MaxTemplateSwitchTotalLengthStrategy
• a_star_aligner::template_switch_distance::strategies::template_switch_total_length::NoTemplateSwitchTotalLengthStrategy
• alignment_configuration::AlignmentConfiguration
• alignment_matrix::AlignmentMatrix
• alignment_matrix::AlignmentMatrixEntry
• alignment_matrix::index::AlignmentMatrixIndex
• alignment_matrix::index::iterators::AlignmentMatrixInnerIterator
• alignment_matrix::index::iterators::AlignmentMatrixQueryIterator
• alignment_matrix::index::iterators::AlignmentMatrixReferenceIterator
• config::BaseCost
• config::TemplateSwitchConfig
• costs::U64Cost
• costs::cost_function::CostFunction
• costs::gap_affine::GapAffineAlignmentCostTable

Enums

• a_star_aligner::alignment_result::AlignmentResult
• a_star_aligner::configurable_a_star_align::ChainingStrategySelector
• a_star_aligner::configurable_a_star_align::DescendantStrategySelector
• a_star_aligner::configurable_a_star_align::MinLengthStrategySelector
• a_star_aligner::configurable_a_star_align::TotalLengthStrategySelector
• a_star_aligner::gap_affine_edit_distance::AlignmentType
• a_star_aligner::template_switch_distance::AlignmentType
• a_star_aligner::template_switch_distance::GapType
• a_star_aligner::template_switch_distance::Identifier
• a_star_aligner::template_switch_distance::TemplateSwitchDirection
• a_star_aligner::template_switch_distance::TemplateSwitchPrimary
• a_star_aligner::template_switch_distance::TemplateSwitchSecondary
• alignment_matrix::BaseAlignmentType
• error::Error

Traits

• a_star_aligner::AlignmentContext
• a_star_aligner::alignment_result::IAlignmentType
• a_star_aligner::alignment_result::alignment::iter::PeekLengthDecreaser
• a_star_aligner::configurable_a_star_align::Alphabet
• a_star_aligner::configurable_a_star_align::alphabets::generic_alphabet::CharacterFromToAsciiTable
• a_star_aligner::template_switch_distance::strategies::AlignmentStrategy
• a_star_aligner::template_switch_distance::strategies::AlignmentStrategySelector
• a_star_aligner::template_switch_distance::strategies::chaining::ChainingStrategy
• a_star_aligner::template_switch_distance::strategies::descendant::TemplateSwitchDescendantStrategy
• a_star_aligner::template_switch_distance::strategies::node_ord::NodeOrdStrategy
• a_star_aligner::template_switch_distance::strategies::primary_match::PrimaryMatchStrategy
• a_star_aligner::template_switch_distance::strategies::primary_range::PrimaryRangeStrategy
• a_star_aligner::template_switch_distance::strategies::secondary_deletion::SecondaryDeletionStrategy
• a_star_aligner::template_switch_distance::strategies::shortcut::ShortcutStrategy
• a_star_aligner::template_switch_distance::strategies::template_switch_count::TemplateSwitchCountStrategy
• a_star_aligner::template_switch_distance::strategies::template_switch_min_length::TemplateSwitchMinLengthStrategy
• a_star_aligner::template_switch_distance::strategies::template_switch_total_length::TemplateSwitchTotalLengthStrategy

Functions

• a_star_aligner::gap_affine_edit_distance_a_star_align
• a_star_aligner::template_switch_distance_a_star_align
• config::io::parse_inf_value

Type Aliases

• error::Result