- d -
- d_callback()
: AW_window
- dangling()
: MatchingOligo
- dangling_char()
: MatchingOligo
- data()
: awt_input_handler
- Data()
: Data
- data()
: DB_scalable
, FINAL_TYPE< SEQTYPE >
, GBENTRY
, MutationsPerSite
, SEC_seq_data
, SeqPart
- data_changed_cb()
: ED4_reference
- DataLoc()
: DataLoc
- db2awar()
: awt_check_box
, awt_radio_button
, awt_string_handler
- db_changed()
: awt_linked_to_item
, awt_string_handler
, FINAL_TYPE< SEQTYPE >
- db_interrupt_data()
: db_interrupt_data
- DB_scalable()
: DB_scalable
- DBerror()
: DBerror
- DbQuery()
: QUERY::DbQuery
- DBwriter()
: DBwriter
- deactivate_plugin()
: ItemShader
- debug_asserter()
: arb_test::debug_asserter
- debug_expectations()
: arb_test::debug_asserter
- debug_get_current()
: MO_Liste
- dec_long()
: chartable::SepBaseFreq
- dec_short()
: chartable::SepBaseFreq
- DecisionTree()
: DecisionTree
- DECLARE_ASSIGNMENT_OPERATOR()
: AlignDataAccess
, AliView
, AP_filter
, AP_weights
, ARB_edge
, arb_test::FINAL_TYPE< T >
, arb_test::match_expectation
, arb_test::predicate_description
, AW_scalar
, ClickedElement
, Code
, CompactedSubSequence
, Convaln_exception
, customCriterion
, Distributor
, ED4_SearchPosition
, Emblref
, ExplicitRange
, FINAL_TYPE< SEQTYPE >
, gb_callback
, gb_triggered_callback
, GenbankRef
, GroupCluster
, MarkedPrefixes
, PaintedNode
, PartialSequence
, Partition
, PlugIn
, PrefixIterator
, PrefixProbabilities
, Range
, RefPtr< T >
, remote_awars
, SequencePosition
, StaticData
, ValueCounter< T >
- DECLARE_DUMP_FOR_BASECLASS()
: ED4_abstract_group_manager
, ED4_abstract_sequence_terminal
, ED4_manager
, ED4_terminal
, ED4_text_terminal
- DECLARE_DUMP_FOR_LEAFCLASS()
: ED4_area_manager
, ED4_bracket_terminal
, ED4_consensus_sequence_terminal
, ED4_device_manager
, ED4_group_manager
, ED4_line_terminal
, ED4_multi_name_manager
, ED4_multi_sequence_manager
, ED4_multi_species_manager
, ED4_name_manager
, ED4_orf_terminal
, ED4_root_group_manager
, ED4_sequence_manager
, FINAL_TYPE< SEQTYPE >
- DECLARE_DUMP_FOR_MIDCLASS()
: ED4_sequence_terminal
- DECLARE_DUMP_FOR_ROOTCLASS()
: ED4_base
- decode_escapes()
: ConfigMapping
- deconstruct_all_trees()
: RootSynchronizer
- deconstruct_weighted()
: DeconstructedTree
- DeconstructedTree()
: DeconstructedTree
- deconstructionPhase()
: RootSynchronizer
- decreasePasses()
: PS_Candidate
- deduceTranslations()
: FINAL_TYPE< SEQTYPE >
- deep_copy()
: SmartPtr< T, C >
- default_is_selected()
: AW_selection_list
- default_select_display()
: AW_subset_selection
- default_select_value()
: AW_subset_selection
- default_toggle()
: awt_radio_button
- defaultColorgroupName()
: ColorGroupDef
- define()
: ED4_reference
, LinePart
- define_canvas_index()
: CanvasRef
- define_dependency()
: ScrollSynchronizer
- DEFINE_DOWNCAST_ACCESSORS()
: FINAL_TYPE< SEQTYPE >
- DEFINE_READ_ACCESSORS()
: AP_main
, ArbParsimony
, TreeNode
, TreeRoot
- define_remote_command()
: AW_root
- DEFINE_TREE_ACCESSORS()
: AP_tree
, ARB_countedTree
, ARB_seqtree
, FINAL_TYPE< SEQTYPE >
- DEFINE_TREE_RELATIVES_ACCESSORS()
: FINAL_TYPE< SEQTYPE >
- DEFINE_TREE_ROOT_ACCESSORS()
: AP_tree_root
, ARB_seqtree_root
, FINAL_TYPE< SEQTYPE >
- defined()
: MatrixOrder
, TextRef
- defined_at()
: HeaderList
- DefinedCommands()
: DefinedCommands
- defineParentOf()
: ParentCache
- degrees()
: AW::Angle
- del_unwanted_entries()
: EntryRemover
- delay_changed_callbacks()
: AW_gc_manager
- DelayReshade()
: DelayReshade
- delbit()
: Bitvector
- Deletable()
: Deletable
- Delete()
: ED4_base
, ED4_manager
, ED4_terminal
- delete_aliEntry_from_SAI()
: AP_pos_var
- delete_by_node()
: TreeRoot
- delete_default()
: AW_selection_list
- delete_element()
: ALI_TLIST< T >
- delete_element_at()
: AW_selection_list
- delete_entries_missing_in_parent()
: AW_subset_selection
- delete_entry()
: AWT_config
, ConfigMapping
- delete_expensive()
: ali_prealigner_mask
- delete_family_list()
: FamilyFinder
- delete_folding_line()
: ED4_foldable
- delete_found_groups()
: GroupSearch
- delete_from_DB()
: FoundGroup
- delete_group()
: GroupSearch
- delete_listed_groups()
: GroupUIdata
- delete_map()
: ALI_SUB_SOLUTION
- delete_member()
: ED4_folding_line
- delete_pointer_2()
: FINAL_TYPE< SEQTYPE >
- delete_requested_by_child()
: ED4_manager
- delete_requested_children()
: ED4_base
, ED4_manager
, ED4_multi_species_manager
, ED4_terminal
- delete_selected_field()
: AWT_configuration
- delete_selected_group()
: GroupUIdata
- delete_value()
: AW_selection_list
- delete_window()
: ED4_window
- deleted()
: DiffLines
- deleted_from_database()
: ED4_base
, ED4_manager
, ED4_sequence_terminal
, ED4_terminal
, ED4_text_terminal
- DeleteOldInsertionData()
: Structure3D
- DeleteOldMoleculeData()
: Structure3D
- DeleteOldSpeciesData()
: Structure3D
- deleteStaticData()
: DBwriter
- deliver()
: ARB_ERROR
- deliverCluster()
: Clusterer
- deliverRest()
: Clusterer
- dependent()
: arb_test::expectation_group
- DepthMarker()
: DepthMarker
- Desco()
: validNames::Desco
- describe()
: arb_test::predicate< FUNC >
, FieldTransfer::ReadRule
, FieldTransfer::WriteRule
- deselect_all()
: ED4_root
- deselect_all_species_and_SAI()
: ED4_multi_species_manager
- deselect_group()
: AWT_graphic_tree
- DesignTargets()
: DesignTargets
- dest()
: ARB_edge
- dest_element()
: DragNDrop
- destroy()
: AP_tree_edge
, TreeNode
- destroy_edges()
: ResourceStack
- destroy_extended()
: GBDATA
- destroy_folding_lines()
: ED4_scrolled_rectangle
- destroy_nodes()
: ResourceStack
- destroy_probe_eval()
: MP_Main
- destroyEdge()
: AP_main
, StackFrameData
- destroyNode()
: AP_main
, AP_tree_root
, CompressionRoot
, FINAL_TYPE< SEQTYPE >
, SimpleRoot
, SizeAwareRoot
, StackFrameData
, TreeRoot
- detach_selected_item()
: InfoWindow
- detect()
: GetMatchesContext
- detect_clusters()
: FINAL_TYPE< SEQTYPE >
- detect_format()
: ArbImporter
- detect_group_state()
: AWT_graphic_tree
- detect_transformation()
: DI_MATRIX
- detectAvailableFields()
: ArbImporter
- detectVerticalGaps()
: export_sequence_data
- DI_ENTRY()
: DI_ENTRY
- DI_GLOBAL_MATRIX()
: DI_GLOBAL_MATRIX
- DI_MATRIX()
: DI_MATRIX
- di_protdist()
: di_protdist
- diagonal()
: AW::Rectangle
- diamond()
: AWT_graphic_tree
- Dict()
: Dict
- didMatch()
: RegMatch
- differs()
: PART
- differs_from()
: AliData
- difflineMode()
: difflineMode
- DiffLines()
: DiffLines
- dimension_awar()
: ShaderPlugin
- disable()
: AW_click_cd
- disconnect()
: NameServerConnection
- disjunct_from()
: PART
- dislocate()
: Group
- dislocate_selected_group()
: AWT_graphic_tree
- display()
: PH_display
- display_node_remark()
: BootstrapConfig
- display_params()
: SEC_root
- display_remark()
: BootstrapConfig
- display_selected_item()
: InfoWindow
- DisplayBasePositions()
: FINAL_TYPE< SEQTYPE >
- displayed()
: PH_display
- DisplayFormat()
: DisplayFormat
- DisplayHelices()
: FINAL_TYPE< SEQTYPE >
- DisplayHelixBackBone()
: FINAL_TYPE< SEQTYPE >
- DisplayHelixMidPoints()
: FINAL_TYPE< SEQTYPE >
- DisplayHelixNumbers()
: FINAL_TYPE< SEQTYPE >
- DisplayMappedSpBasePositions()
: FINAL_TYPE< SEQTYPE >
- DisplayMappedSpInsertions()
: FINAL_TYPE< SEQTYPE >
- DisplayMolecule()
: FINAL_TYPE< SEQTYPE >
- DisplayMoleculeMask()
: FINAL_TYPE< SEQTYPE >
- DisplayMoleculeName()
: FINAL_TYPE< SEQTYPE >
- displayName()
: ArbProbe
- distance_to_tree_center()
: PART
- distanceSum()
: Multiroot
- distanceTo()
: PART
- distanceToCenterSum()
: Multiroot
- distinct_from()
: AW::Rectangle
- distribute_children()
: ED4_manager
- Distributor()
: Distributor
- dna_at()
: FailedAt
- DNA_Table()
: DNA_Table
- do_accept_missing_data()
: FilteredExport
- do_align()
: FINAL_TYPE< SEQTYPE >
- do_callbacks()
: FINAL_TYPE< SEQTYPE >
- do_drag()
: Dragged
- do_drop()
: Dragged
- do_lazy_load()
: AP_sequence
- do_postcalc_callback()
: ST_ML
- do_reserve()
: PS_BitMap
- do_scale()
: BranchLinewidthScaler
- does_bootstrap()
: AP_filter
- does_exist()
: AW_clicked_element
- does_shade()
: AP_TreeShader
- doesMatch()
: GroupPenalty
- doesRemap()
: MG_remaps
- DoHelixMapping()
: FINAL_TYPE< SEQTYPE >
- domainLength()
: MatchingOligo
- domainPossible()
: MatchingOligo
- domainSeen()
: MatchingOligo
- done()
: arb_progress
, ArbProgress::counter
, ArbProgress::nestable
, ExecutingMacro
, FINAL_TYPE< SEQTYPE >
, null_counter
, Partition
, PrefixIterator
- dont_bind_rest()
: MatchingOligo
- dont_close()
: BufferedPipeReader
- dont_save_awars_with_default_value()
: AW_root
- dont_suppress()
: SuppressOutput
- Dots()
: Dots
- drag_target_detection()
: AWT_graphic
- Dragged()
: Dragged
- DragNDrop()
: DragNDrop
- draw()
: ED4_bracket_terminal
, ED4_CursorShape
, ED4_line_terminal
, ED4_terminal
, ED4_text_terminal
, FINAL_TYPE< SEQTYPE >
- draw_bb()
: ED4_base
- draw_branch_line()
: AWT_graphic_tree
- draw_drag_box()
: ED4_terminal
- draw_drag_indicator()
: Dragged
, DragNDrop
, FINAL_TYPE< SEQTYPE >
, Scaler
- draw_line()
: AW_window
- draw_scale_indicator()
: BranchLinewidthScaler
- draw_text()
: FINAL_TYPE< SEQTYPE >
- draw_top_separator_once()
: IRS_data
- DrawBox()
: FINAL_TYPE< SEQTYPE >
- drawn_after()
: SEC_drawn_positions
- drawn_at()
: SEC_drawn_positions
- drawn_at_or_after()
: SEC_drawn_positions
- drawn_before()
: SEC_drawn_positions
- drawnSize()
: SEC_constrainted
- drop()
: ExecutingMacro
- dt_bondssum()
: dt_bondssum
- dump()
: arb_progress
, arb_test::group_match
, ArbProgress::counter
, ArbProgress::nestable
, BackTraceInfo
, FastAlignInsertion
, FastAlignReport
, InsertPerfMeter
, OptiPerfMeter
, PartialSequence
, ProbeIterator
, PT_statistic
- dump_at_position()
: AW_window
- dump_brief_description()
: arb_test::expectation
, arb_test::expectation_group
, arb_test::FINAL_TYPE< T >
, arb_test::match_expectation
, arb_test::matcher
, arb_test::value_matcher< T >
- dump_cursor_pos()
: Data
- dump_error()
: ModRLimit
- dump_expectation()
: arb_test::FINAL_TYPE< T >
, arb_test::matcher
, arb_test::value_matcher< T >
- dump_num_of()
: arb_test::group_match
- dump_some_expectations()
: arb_test::expectation_group
- dump_to()
: MemDump
- dumpAll()
: FastAlignInsertion
- dumpCustom()
: InsertPerfMeter
, OptiPerfMeter
- dup()
: AP_combinableSeq
, AP_sequence
, AP_sequence_simple_protein
, FINAL_TYPE< SEQTYPE >
, MostLikelySeq
- dup_corresponding_part()
: PosRange
- DupCriteria()
: DupCriteria
- duplicate()
: probe_combi_statistic
, probe_tabs
- duplicate_list()
: List< Type >
- DuplicateLinkFilter()
: DuplicateLinkFilter
- DupNameCriterion()
: DupNameCriterion