Augustus 3.4.0
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Class Index
A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W
A
adl_serializer (nlohmann)
AliEdge
Alignment
AlignmentElement (SS)
AlignmentRow
AliGraph
AliNode
AliPath
AltGene
Ancestor
AnnoSeqGeneIterator
AnnoSequence
Annotation
AugustusGraph
B
BacktrackAlignDB (SS)
BaseCount
basic_json (nlohmann)
BaumWelch
binary_reader (nlohmann::detail)
binary_writer (nlohmann::detail)
BinnedMMGroup
Bitmask
Block (PP)
BlockScoreType (PP)
BonusProbEntry (PP)
BonusProbType (PP)
boundaries (nlohmann::detail::dtoa_impl)
byte_container_with_subtype (nlohmann)
C
cached_power (nlohmann::detail::dtoa_impl)
CandidateCollection (PP)
Cell (SS)
CodonEvo
CodonEvoDiscr
CodonMSA
Column (PP)
CompareBoundaryFragment
CompareStatePathPtr
CompGenePred
Composition
conjunction (nlohmann::detail)
conjunction< B1 > (nlohmann::detail)
conjunction< B1, Bn... > (nlohmann::detail)
Constant
ContentDecomposition
ContentModel
ContentStairs
CRF
cumValues
D
DbSeqAccess
detector (nlohmann::detail)
detector< Default, void_t< Op< Args... > >, Op, Args... > (nlohmann::detail)
dfs_time_visitor
Dist
DistanceType (PP)
diyfp (nlohmann::detail::dtoa_impl)
DNA (PP)
E
Edge
EHMMTraining
EOPList
Evaluation
Evidence
Evo
exception (nlohmann::detail)
ExonCandidate
ExonEvo
ExonModel
ExonModelError
ExonScorer (PP)
external_constructor (nlohmann::detail)
external_constructor< value_t::array > (nlohmann::detail)
external_constructor< value_t::binary > (nlohmann::detail)
external_constructor< value_t::boolean > (nlohmann::detail)
external_constructor< value_t::number_float > (nlohmann::detail)
external_constructor< value_t::number_integer > (nlohmann::detail)
external_constructor< value_t::number_unsigned > (nlohmann::detail)
external_constructor< value_t::object > (nlohmann::detail)
external_constructor< value_t::string > (nlohmann::detail)
F
Feature
FeatureCollection
FeatureTypeInfo
file_input_adapter (nlohmann::detail)
fragment
FramedPatMMGroup
FreqSegment
from_json_fn (nlohmann::detail)
FsHitCollection (PP)
FsHitType (PP)
FsSeedCollection (PP)
G
GBError
GBFeature
GBPositions
GBProcessor
GBSplitter
Gene
GeneMSA
GeneticCode
GenomicMSA
Goto_line_after
Graph
H
has_from_json (nlohmann::detail)
has_from_json< BasicJsonType, T, enable_if_t< !is_basic_json< T >::value > > (nlohmann::detail)
has_non_default_from_json (nlohmann::detail)
has_non_default_from_json< BasicJsonType, T, enable_if_t< !is_basic_json< T >::value > > (nlohmann::detail)
has_to_json (nlohmann::detail)
has_to_json< BasicJsonType, T, enable_if_t< !is_basic_json< T >::value > > (nlohmann::detail)
hash< nlohmann::json > (std)
HelpException
HintGroup
HitSequence (PP)
HitSequenceCollection (PP)
HitSequenceList (PP)
HitSequenceNode (PP)
I
IdxSortCriterion
IGenicModel
IGenicModelError
index_sequence (nlohmann::detail)
input_stream_adapter (nlohmann::detail)
internal_iterator (nlohmann::detail)
IntronModel
IntronModelError
IntronProfile (PP)
invalid_iterator (nlohmann::detail)
InvalidNucleotideError
is_basic_json (nlohmann::detail)
is_basic_json< NLOHMANN_BASIC_JSON_TPL > (nlohmann::detail)
is_compatible_array_type (nlohmann::detail)
is_compatible_array_type_impl (nlohmann::detail)
is_compatible_array_type_impl< BasicJsonType, CompatibleArrayType, enable_if_t< is_detected< value_type_t, CompatibleArrayType >::value &&is_detected< iterator_t, CompatibleArrayType >::value &&!is_iterator_traits< iterator_traits< CompatibleArrayType > >::value > > (nlohmann::detail)
is_compatible_integer_type (nlohmann::detail)
is_compatible_integer_type_impl (nlohmann::detail)
is_compatible_integer_type_impl< RealIntegerType, CompatibleNumberIntegerType, enable_if_t< std::is_integral< RealIntegerType >::value &&std::is_integral< CompatibleNumberIntegerType >::value &&!std::is_same< bool, CompatibleNumberIntegerType >::value > > (nlohmann::detail)
is_compatible_object_type (nlohmann::detail)
is_compatible_object_type_impl (nlohmann::detail)
is_compatible_object_type_impl< BasicJsonType, CompatibleObjectType, enable_if_t< is_detected< mapped_type_t, CompatibleObjectType >::value &&is_detected< key_type_t, CompatibleObjectType >::value > > (nlohmann::detail)
is_compatible_string_type (nlohmann::detail)
is_compatible_string_type_impl (nlohmann::detail)
is_compatible_string_type_impl< BasicJsonType, CompatibleStringType, enable_if_t< is_detected_exact< typename BasicJsonType::string_t::value_type, value_type_t, CompatibleStringType >::value > > (nlohmann::detail)
is_compatible_type (nlohmann::detail)
is_compatible_type_impl (nlohmann::detail)
is_compatible_type_impl< BasicJsonType, CompatibleType, enable_if_t< is_complete_type< CompatibleType >::value > > (nlohmann::detail)
is_complete_type (nlohmann::detail)
is_complete_type< T, decltype(void(sizeof(T)))> (nlohmann::detail)
is_constructible_array_type (nlohmann::detail)
is_constructible_array_type_impl (nlohmann::detail)
is_constructible_array_type_impl< BasicJsonType, ConstructibleArrayType, enable_if_t< !std::is_same< ConstructibleArrayType, typename BasicJsonType::value_type >::value &&std::is_default_constructible< ConstructibleArrayType >::value &&(std::is_move_assignable< ConstructibleArrayType >::value||std::is_copy_assignable< ConstructibleArrayType >::value)&&is_detected< value_type_t, ConstructibleArrayType >::value &&is_detected< iterator_t, ConstructibleArrayType >::value &&is_complete_type< detected_t< value_type_t, ConstructibleArrayType > >::value > > (nlohmann::detail)
is_constructible_array_type_impl< BasicJsonType, ConstructibleArrayType, enable_if_t< std::is_same< ConstructibleArrayType, typename BasicJsonType::value_type >::value > > (nlohmann::detail)
is_constructible_object_type (nlohmann::detail)
is_constructible_object_type_impl (nlohmann::detail)
is_constructible_object_type_impl< BasicJsonType, ConstructibleObjectType, enable_if_t< is_detected< mapped_type_t, ConstructibleObjectType >::value &&is_detected< key_type_t, ConstructibleObjectType >::value > > (nlohmann::detail)
is_constructible_string_type (nlohmann::detail)
is_constructible_string_type_impl (nlohmann::detail)
is_constructible_string_type_impl< BasicJsonType, ConstructibleStringType, enable_if_t< is_detected_exact< typename BasicJsonType::string_t::value_type, value_type_t, ConstructibleStringType >::value > > (nlohmann::detail)
is_constructible_tuple (nlohmann::detail)
is_constructible_tuple< T1, std::tuple< Args... > > (nlohmann::detail)
is_getable (nlohmann::detail)
is_iterator_of_multibyte (nlohmann::detail)
is_iterator_traits (nlohmann::detail)
is_iterator_traits< iterator_traits< T > > (nlohmann::detail)
is_json_ref (nlohmann::detail)
is_json_ref< json_ref< T > > (nlohmann::detail)
is_sax (nlohmann::detail)
is_sax_static_asserts (nlohmann::detail)
iter_impl (nlohmann::detail)
iteration_proxy (nlohmann::detail)
iteration_proxy_value (nlohmann::detail)
HitSequenceNode::iterator (PP)
iterator_input_adapter (nlohmann::detail)
iterator_input_adapter_factory (nlohmann::detail)
iterator_input_adapter_factory< IteratorType, enable_if_t< is_iterator_of_multibyte< IteratorType >::value > > (nlohmann::detail)
iterator_traits (nlohmann::detail)
iterator_traits< T *, enable_if_t< std::is_object< T >::value > > (nlohmann::detail)
iterator_traits< T, enable_if_t< !std::is_pointer< T >::value > > (nlohmann::detail)
iterator_types (nlohmann::detail)
iterator_types< It, void_t< typename It::difference_type, typename It::value_type, typename It::pointer, typename It::reference, typename It::iterator_category > > (nlohmann::detail)
J
json_pointer (nlohmann)
json_ref (nlohmann::detail)
json_reverse_iterator (nlohmann::detail)
json_sax (nlohmann)
json_sax_acceptor (nlohmann::detail)
json_sax_dom_callback_parser (nlohmann::detail)
json_sax_dom_parser (nlohmann::detail)
K
KeyNotFoundError
L
HitSequenceNode::last_iterator (PP)
less<::nlohmann::detail::value_t > (std)
LessDereference
lexer (nlohmann::detail)
lexer_base (nlohmann::detail)
LiftOver
LLDouble
LocusTree
LogDouble
M
make_index_sequence (nlohmann::detail)
make_index_sequence< 0 > (nlohmann::detail)
make_index_sequence< 1 > (nlohmann::detail)
make_void (nlohmann::detail)
Match (PP)
Matrix
MEApath
MemSeqAccess
merge_and_renumber (nlohmann::detail)
merge_and_renumber< index_sequence< I1... >, index_sequence< I2... > > (nlohmann::detail)
MMGroup
Motif
MsaInsertion
MsaSignature
MultiTargetExonScorer (PP)
N
NAMGene
NAMGeneError
NcModel
NcModelError
Node
nonesuch (nlohmann::detail)
NoSubmapFoundError
O
OpenReadingFrame
OptionListItem
OptionsList
ordered_map (nlohmann)
ORF
OrthoExon
OrthoGene
OrthoGraph
other_error (nlohmann::detail)
out_of_range (nlohmann::detail)
output_adapter (nlohmann::detail)
output_adapter_protocol (nlohmann::detail)
output_stream_adapter (nlohmann::detail)
output_string_adapter (nlohmann::detail)
output_vector_adapter (nlohmann::detail)
P
Parameters
parse_error (nlohmann::detail)
parser (nlohmann::detail)
Parsimony
PartParseError (PP)
PartScoreType (PP)
PatMMGroup
PhyloTree
posElements
Position (PP)
position_t (nlohmann::detail)
PredictionRun
PredictionScheme
PrflAlignment (SS)
primitive_iterator_t (nlohmann::detail)
priority_tag (nlohmann::detail)
priority_tag< 0 > (nlohmann::detail)
Profile (PP)
ProfileInsigError (PP)
ProfileMap
ProfileNotFoundError (PP)
ProfileParseError (PP)
ProfileReadError (PP)
ProjectError
Properties
PropertiesError
ProteinSequence (SS)
ptr_comparison
R
RandSeqAccess
Range (PP)
HitSequenceNode::reverse_iterator (PP)
Row (SS)
S
ScoringCandidate (PP)
SegProbs
SegSortCriterion
Seq2Int
SeqIntKey
SequenceFeatureCollection
serializer (nlohmann::detail)
Match::shift (PP)
SimilarityMatrix (SS)
SimilarityScore (SS)
SingleTargetExonScorer (PP)
Smooth
SnippetList
SnippetListItem
SnippetProbs
SortCriterion
span_input_adapter (nlohmann::detail)
SpeciesCollection
SpeciesGraph
SpecifiedTypeError
SQLiteDB
SrcEvidence
State
Statement
StateModel
StatePath
StatePathCollection
static_const (nlohmann::detail)
Status
StringAlignment
SubmapEmptyError
SubstateId
SubstateModel (PP)
T
to_json_fn (nlohmann::detail)
Tokenizer
train_data
TrainingData
Transcript
Treenode
tuple_element< N, ::nlohmann::detail::iteration_proxy_value< IteratorType > > (std)
tuple_size<::nlohmann::detail::iteration_proxy_value< IteratorType > > (std)
twomer (PP)
type_error (nlohmann::detail)
U
UtrModel
UtrModelError
V
ValueError
ValueFormatError
ViterbiColumnType
ViterbiEntryType
ViterbiMatrixType
ViterbiSubmapBasetype
ViterbiSubmapEntry
ViterbiSubmapType
W
wide_string_input_adapter (nlohmann::detail)
wide_string_input_helper (nlohmann::detail)
wide_string_input_helper< BaseInputAdapter, 2 > (nlohmann::detail)
wide_string_input_helper< BaseInputAdapter, 4 > (nlohmann::detail)