- s -
- s()
: AW_hsv
- S2str()
: AWT_translator
- S2strArray()
: AWT_translator
- safe_remove()
: CharPtrArray
- SAI_graphic()
: SAI_graphic
- SAI_selection()
: SAI_selection
- SAI_sellst_spec()
: SAI_sellst_spec
- SaiAciApplicator()
: SaiAciApplicator
- SaiBoolchainOperator()
: SaiBoolchainOperator
- SaiBoolRule()
: SaiBoolRule
- SaiCalcEnv()
: SaiCalcEnv
- SaiCalculator()
: SaiCalculator
- SaiMatrixTranslator()
: FINAL_TYPE< SEQTYPE >
- SaiOperator()
: SaiOperator
- saiProbeData()
: saiProbeData
- SAIs_visualized()
: ED4_host
, ED4_plugin_host
- SaiTranslator()
: FINAL_TYPE< SEQTYPE >
- same_function_as()
: Callback_FFV< RT, F1, F2 >
, Callback_FVF< RT, F1, F2 >
, Callback_FVV< RT, FIXED >
, Callback_VV< RT >
- sameObject()
: SmartPtr< T, C >
- Sampler()
: Sampler
- save()
: AW_selection_list
- Save()
: AWT_configuration
- save()
: ComplementLocation
, DI_MATRIX
, FileContent
, FINAL_TYPE< SEQTYPE >
, GBT_config
, JoinedLocation
, Location
, PS_BitMap
, PS_BitSet
, PS_Candidate
, PS_Node
, SEC_region
, SimpleLocation
, StorableSelectionList
- save_aliEntry_to_SAI()
: AP_pos_var
- save_as()
: GB_MAIN_TYPE
- save_changes()
: KeySorter
- save_modified_tree()
: GroupBuilder
- save_properties()
: AW_root
- save_quick()
: GB_MAIN_TYPE
- save_quick_as()
: GB_MAIN_TYPE
- save_to_DB()
: AWT_graphic
, AWT_graphic_tree
, AWT_nonDB_graphic
, FINAL_TYPE< SEQTYPE >
- saveAs()
: FileContent
- saveASCII()
: PS_Node
- saveAsOver()
: GBT_config
- saveFromTill()
: ArbDBWriter
- saveReadConfig()
: FieldTransfer::ReadRule
- saveSAI()
: FINAL_TYPE< SEQTYPE >
- saveString()
: ArbStringCache
- saveTo()
: FieldTransfer::RuleSet
, FINAL_TYPE< SEQTYPE >
- saveToDB()
: AP_tree_root
, ARB_seqtree_root
, FINAL_TYPE< SEQTYPE >
- saveWriteConfig()
: FieldTransfer::WriteRule
- saveXML()
: ArbProbeCollection
- scale()
: probe_combi_statistic
- scale_branchlengths()
: TreeNode
- Scaler()
: Scaler
- scaler2awar()
: AW_ScalerTransformer
- scaling()
: Scaler
- scan()
: parameters
- scan_display_widths()
: Cluster
- scan_value_range_cb()
: ItemFieldShader
- scanFields()
: AvailableFieldScanner
, ExportFieldScanner
, ImportFieldScanner
, MergeFieldScanner
- screen_to_sequence()
: ED4_remap
- ScreenToWinCoordinates()
: FINAL_TYPE< SEQTYPE >
- scroll()
: AWT_canvas
, ED4_scrolled_rectangle
- scroll_cells()
: MatrixDisplay
- scroll_into_view()
: ED4_terminal
- scroll_rectangle()
: ED4_window
- scrollbars_and_scrolledRect_inSync()
: ED4_window
- ScrollSynchronizer()
: ScrollSynchronizer
- search()
: ED4_SearchResults
- search_best_match()
: SpecSetRegistry
- search_ID()
: ED4_base
, ED4_manager
, ED4_terminal
- search_member()
: ED4_container
- search_remote_command()
: AW_root
- search_spec_child_rek()
: ED4_manager
- search_target_species()
: ED4_container
- search_windows()
: search_windows
- searchAgain()
: ED4_SearchResults
- SearchedTree()
: SearchedTree
- searchFamily()
: FamilyFinder
, PT_FamilyFinder
- SearchFIFO()
: SearchFIFO
- SearchRelativeParams()
: SearchRelativeParams
- SearchRelativesReference()
: SearchRelativesReference
- SearchSettings()
: SearchSettings
- SearchTree()
: SearchTree
- SearchTreeNode()
: SearchTreeNode
- SEC_base()
: SEC_base
- SEC_base_iterator()
: SEC_base_iterator
- SEC_base_part()
: SEC_base_part
- SEC_base_part_iterator()
: SEC_base_part_iterator
- SEC_bond_def()
: SEC_bond_def
- SEC_constrainted()
: SEC_constrainted
- SEC_db_interface()
: SEC_db_interface
- SEC_dbcb()
: SEC_dbcb
- SEC_displayParams()
: SEC_displayParams
- SEC_graphic()
: FINAL_TYPE< SEQTYPE >
- SEC_helix()
: FINAL_TYPE< SEQTYPE >
- SEC_helix_strand()
: FINAL_TYPE< SEQTYPE >
- SEC_loop()
: FINAL_TYPE< SEQTYPE >
- SEC_oriented()
: SEC_oriented
- SEC_region()
: SEC_region
- SEC_root()
: SEC_root
- SEC_segment()
: FINAL_TYPE< SEQTYPE >
- SEC_segment_iterator()
: SEC_segment_iterator
- SEC_seq_data()
: SEC_seq_data
- sec_since()
: ARB_timestamp
- SEC_strand_const_iterator()
: SEC_strand_const_iterator
- SEC_strand_iterator()
: SEC_strand_iterator
- SEC_structure_toggler()
: SEC_structure_toggler
- second()
: TwoLeafs
- secroot()
: SEC_db_interface
- Section()
: FINAL_TYPE< SEQTYPE >
- security_awar()
: AliAdmin
- security_name()
: AliAdmin
- seen()
: LimitTracker< T >
- seenDups()
: ID_checker
- select_all()
: ED4_multi_species_manager
- select_awar()
: AliAdmin
- select_default()
: AW_selection_list
- select_element_at()
: AW_selection_list
- select_first()
: SpeciesSelector
- select_group()
: AWT_graphic_tree
- select_mode()
: AW_window
- select_name()
: AliAdmin
- select_next()
: SpeciesSelector
- selected_plugin_changed_cb()
: FINAL_TYPE< SEQTYPE >
- selected_range_changed_cb()
: FINAL_TYPE< SEQTYPE >
- selected_species_mark()
: ED4_multi_species_manager
- SelectedDatabase()
: SelectedDatabase
- SelectionListSpec()
: SelectionListSpec
- selects()
: ARB_tree_predicate
- self()
: SEC_base
, SEC_base_part
- self_ref()
: TreeNode
- send_update_to_server()
: GB_MAIN_TYPE
- sens_mask()
: AW_window
- sep______________()
: AW_window
- SepBaseFreq()
: chartable::SepBaseFreq
- Seq()
: Seq
- seq_2_helix()
: AW_helix
- seq_done()
: FileWriter
- SeqInfo()
: SeqInfo
- SeqPart()
: SeqPart
- sequence()
: ALI_MAP
, ALI_NORM_SEQUENCE
, ALI_PREALIGNER
, ALI_PROFILE
, ALI_SEQUENCE
, ArbProbe
, ED4_reference_terminals
, FastSearchOccurrence
, FastSearchSequence
, ProbeOccurrence
, SEC_seq_data
, SequencePosition
- sequence2base_position()
: ED4_cursor
- sequence_change()
: MostLikelySeq
- sequence_info()
: ED4_reference_terminals
- sequence_length()
: ALI_PROFILE
- sequence_to_screen()
: ED4_remap
- sequence_to_screen_PLAIN()
: ED4_remap
- sequence_without_inserts()
: ALI_MAP
, ALI_PREALIGNER
- SequenceAliData()
: SequenceAliData
- SequenceBuffer()
: SequenceBuffer
- SequenceHandler()
: SequenceHandler
- SequenceIterator()
: SequenceIterator
- SequencePosition()
: SequencePosition
- set()
: AISC_Object
, ALI_MAP
, ALI_PATHMAP
, ALI_TARRAY< T >
, AlignBuffer
, AP_matrix
, AP_sequence
, AW::Vector
, DefinedCommands
- Set()
: ED4_species_pointer
- set()
: FINAL_TYPE< SEQTYPE >
- Set()
: FINAL_TYPE< SEQTYPE >
- set()
: PS_BitMap
- Set()
: PS_BitSet
- set()
: SetOnce
, SetVariables
, ST_rate_matrix
, symmetric_matrix< T >
- SET_aaColor()
: ED4_orf_terminal
- SET_aaSeqFlags()
: ED4_orf_terminal
- SET_aaSequence()
: ED4_orf_terminal
- set_aborted()
: InsertData
- set_abs_angle()
: SEC_oriented
- set_abs_pos()
: AbsLoc
- set_abs_x()
: ED4_cursor
- set_act_gen()
: ProbeValuation
- set_active()
: AW_root
- set_alignment_length()
: FINAL_TYPE< SEQTYPE >
- set_angle()
: AngleBuffer
, AP_tree
- set_AW_cb_guards()
: AW_cb
- set_AW_postcb_cb()
: AW_cb
- set_awar_value()
: AW_selection_list
, ConfigDefinition
- set_background()
: AW_window
- set_bitkennung()
: Sonde
- set_block_token()
: TokenListBlock
- set_bootstrap()
: TreeNode
- set_bootstrap_seen()
: TreeRoot
- set_both_links()
: ED4_base
- set_bottom_area_height()
: AW_window
- set_bottom_clip_border()
: AW_clipable
- set_bottom_clip_margin()
: AW_clipable
- set_bottom_font_overlap()
: AW_clipable
- set_branchlength()
: TreeNode
- set_branchlength_preserving()
: TreeNode
- set_branchlength_unrooted()
: TreeNode
- set_cache_sizes()
: probe_input_data
- set_case_sensitive()
: ED4_reference
- set_cd1()
: AW_click_cd
- set_cd2()
: AW_click_cd
- set_center()
: FINAL_TYPE< SEQTYPE >
- set_change()
: gb_header_flags
- set_changed_cb()
: AW_gc_manager
, DI_GLOBAL_MATRIX
- set_char_bind()
: BI_pairdef
- set_char_size()
: AW_GC
- set_clear_at_refresh()
: ED4_update_info
- set_click_time()
: AW_area_management
- set_clipall()
: AW_clipable
- set_cliprect()
: AW_clipable
- set_cluster_id()
: FoundGroup
- set_color_mode()
: FINAL_TYPE< SEQTYPE >
- set_command()
: Code
- set_comment()
: GBT_config
- set_config()
: AWT_configuration
- set_consider_text_for_zoom_reset()
: AWT_canvas
- set_content_from()
: OrgInfo
, RDP_comments
, SeqInfo
- set_current_ARC()
: List< Type >
- set_cursor()
: AW_root_Motif
, Data
, PH_display_status
, SEC_root
- set_cursor_x()
: PH_display_status
- set_data()
: gb_extern_data
- set_db_4_nameserver()
: ArbImporter
- set_default_padding()
: AWT_graphic_exports
- set_definition()
: GBT_config
- set_descriptions()
: AP_userdef_matrix
- set_dimension()
: ED4_folding_line
, SpeciesFlag
- set_discretion_factor()
: DB_scalable
- set_display_style()
: GEN_graphic
- set_displayed()
: AW_selection_list_entry
, AW_selection_list_iterator
- set_double_click_callback()
: AW_area_management
, AW_window
- set_downdist()
: NodeLeafDistance
- set_dragEndpoint()
: AWT_canvas
- set_elem()
: list_elem< Type >
- set_entry()
: AWT_config
, ConfigMapping
- set_equilateral_default_padding()
: AWT_graphic_exports
- set_error()
: AliData
, Writer
- set_expose_callback()
: AW_area_management
, AW_window
- set_extra_text_padding()
: AWT_graphic_exports
- set_failure()
: Realigner
- set_faked_weight()
: PART
- set_far()
: Sonde
- set_father()
: POS_TREE1
- set_fg_color()
: AW_GC
- set_file_suffix()
: AW_selection_list
- set_filter()
: AW_device
- set_first_header()
: HeaderList
- set_fixpoint_strand()
: FINAL_TYPE< SEQTYPE >
- set_float()
: AW_scalar
- set_focus_callback()
: AW_window
- set_font()
: AW_GC
, AW_stylable
- set_font_overlap()
: AW_clipable
- set_foreground_color()
: AW_stylable
- set_function()
: AW_GC
, AW_stylable
- set_gap_handling()
: ED4_reference
- set_gauge()
: BasicStatus
- set_gb_main()
: MO_Liste
- set_gb_tree()
: ARB_seqtree_root
- set_gb_tree_and_name()
: ARB_seqtree_root
- set_GeneName()
: GEN_root
- set_grey_level()
: AW_GC_config
, AW_stylable
- set_group_state()
: probe_input_data
- set_handled()
: ARB_ERROR
- set_header_ACI()
: FilteredExport
- set_helix()
: FINAL_TYPE< SEQTYPE >
- set_highlighted()
: FINAL_TYPE< SEQTYPE >
- set_horizontal_change_callback()
: AW_window
- set_horizontal_font_overlap()
: AW_clipable
- set_horizontal_scrollbar_left_indent()
: AW_window
- set_horizontal_scrollbar_position()
: AW_window
, AWT_canvas
- set_id()
: Seq
- set_indent()
: Formatter
- set_info()
: BranchWindow
- set_info_area_height()
: AW_window
- set_input_callback()
: AW_area_management
, AW_window
- set_int()
: AW_scalar
- set_item()
: awt_linked_to_item
- set_last_drawed_cursor_position()
: SEC_root
- set_last_widget()
: AW_root_Motif
- set_LatestSon()
: FINAL_TYPE< SEQTYPE >
- set_left_clip_border()
: AW_clipable
- set_left_font_overlap()
: AW_clipable
- set_len()
: PART
- set_length()
: ARB_edge
, AW::Vector
, Generation
- set_line()
: Reader
- set_line_attributes()
: AW_GC
, AW_stylable
- set_line_attributes_for()
: AWT_graphic_tree
- set_line_start()
: Parser
- set_linewidth()
: AP_tree
- set_linewidth_recursive()
: AP_tree
- set_links()
: ED4_base
- set_loc()
: ChainIteratorStage1::_U::_L
, ChainIteratorStage1::_U::_S
- set_logical_root_to()
: AWT_graphic_tree
- set_loop()
: FINAL_TYPE< SEQTYPE >
- set_marker_display()
: AWT_graphic_tree
- set_marks_in_found_groups()
: GroupSearch
- set_marks_in_group()
: GroupSearch
- set_max()
: AW_awar
, DB_scalable
- set_memblock()
: ConstStrArray
- set_min()
: AW_awar
, DB_scalable
- set_min_wanted_words()
: DupNameCriterion
- set_minmax()
: AW_awar
- set_mismatch_at_pos()
: Hit
- set_mismatches()
: SearchTreeNode
- set_mode()
: AWT_canvas
, ED4_remap
- set_modified()
: ST_ML
- set_mor()
: Sonde
- set_motion_callback()
: AW_area_management
, AW_window
- set_name()
: AbsLoc
, awt_mask_item
- set_next()
: ED4_list_elem< T >
, Header
, list_elem< Type >
- set_next_segment()
: FINAL_TYPE< SEQTYPE >
- set_next_strand()
: FINAL_TYPE< SEQTYPE >
- set_no_char_size()
: AW_GC
- set_node_deleted_callback()
: AP_tree_root
- set_nodiff_indicator()
: ED4_reference
- set_offset()
: AW_zoomable
- set_on_extra_line()
: FINAL_TYPE< SEQTYPE >
- set_origin()
: PART
, PH_display_status
- set_origin_loop()
: FINAL_TYPE< SEQTYPE >
- set_p_eval()
: MP_Main
- set_pairs_def()
: BI_pairdef
- set_parameters()
: FINAL_TYPE< SEQTYPE >
- set_params_checked()
: GBL_command_arguments
- set_parent()
: Token
, TokenList
- set_pointer()
: AW_scalar
, UnitPtr
- set_popup_callback()
: AW_window
- set_pos()
: ED4_folding_line
, list_elem< Type >
, LocationEditor
- set_pos_for()
: CentigradePos
- set_position()
: DataLoc
- set_postcalc_callback()
: ST_ML
- set_prev()
: list_elem< Type >
- set_probe_combi()
: probe_combi_statistic
- set_probe_region_offset()
: ProbeMatch_impl
- set_property()
: ED4_base
- set_query()
: NN_GlobalData
- set_query_to_update()
: ScopedTransporter
- set_range()
: ED4_block
, FINAL_TYPE< SEQTYPE >
- set_ranges()
: StaticData
- set_recording()
: BoundActionTracker
- set_rect()
: ED4_scrolled_rectangle
- set_rect_and_update_folding_line_positions()
: ED4_scrolled_rectangle
- set_ref_sequence()
: FINAL_TYPE< SEQTYPE >
- set_refresh()
: ED4_update_info
, ST_ML
- set_rel_angle()
: SEC_oriented
- set_reload_on_reinit()
: FINAL_TYPE< SEQTYPE >
- set_remark()
: TreeNode
- set_remembered_as_current_ARC()
: List< Type >
- set_report()
: SearchTreeNode
- set_required_baseCount()
: FilteredExport
- set_resize()
: ED4_update_info
- set_resize_callback()
: AW_area_management
, AW_window
- set_result_list()
: NN_GlobalData
- set_right_clip_border()
: AW_clipable
- set_right_font_overlap()
: AW_clipable
- set_root()
: AP_tree_edge
, ARB_edge
, FINAL_TYPE< SEQTYPE >
, SEC_root
, TreeNode
- set_root_changed_callback()
: AP_tree_root
- set_root_loop()
: SEC_root
- set_scalerType()
: VarUpdateInfo
- set_screen()
: AW_common
- set_screen_relative_pos()
: ED4_cursor
- set_screen_size()
: AW_common
- set_scrollbars()
: AWT_canvas
- set_scrolled_rectangle()
: ED4_window
- set_secstruct_display()
: ED4_sequence_terminal
- set_sellist()
: VarUpdateInfo
- set_seq()
: ARB_seqtree
- set_sequence()
: MostLikelySeq
- set_sequence_ACI()
: FilteredExport
- set_sequence_portion()
: SEC_base_part
, SEC_region
- set_show_constraints()
: SEC_root
- set_single_mode()
: export_sequence_data
- set_size_does_change()
: ED4_extension
- set_slider_max()
: MatrixDisplay
- set_slider_min()
: MatrixDisplay
- set_source()
: Parser
- set_space()
: CharPtrArray
- set_species()
: AW_trackPositions_device
- set_species_data()
: FINAL_TYPE< SEQTYPE >
- set_species_name()
: GcgWriter
- set_species_pointer()
: ED4_base
- set_srt()
: AW_awar
- set_standard_default_padding()
: AWT_graphic_exports
- set_start_offset()
: SearchTreeNode
- set_status()
: LocationEditor
- set_stc()
: MP_Main
- set_string()
: AW_scalar
- set_subtitle()
: BasicStatus
- set_tab()
: Formatter
, PH_display_status
- set_tabstop()
: Formatter
- set_temp_if_is_default()
: AW_awar
- set_text()
: ArbProgress::nestable
, FINAL_TYPE< SEQTYPE >
, initial_progress
, null_progress
- set_threshold()
: FINAL_TYPE< SEQTYPE >
- set_to_terminal()
: ED4_cursor
- set_toAlign_sequence()
: FINAL_TYPE< SEQTYPE >
- set_tokens()
: Data
- set_top_clip_border()
: AW_clipable
- set_top_font_overlap()
: AW_clipable
- set_top_middle_line_terminal()
: FINAL_TYPE< SEQTYPE >
- set_top_middle_spacer_terminal()
: FINAL_TYPE< SEQTYPE >
- set_touched_idx()
: GBCONTAINER
- set_tracking()
: UserActionTracker
- set_tracking_according_to()
: ClientActionTracker
- set_transferUndefFields()
: FieldTransfer::RuleSet
- set_tree()
: ArbParsimony
- set_tree_awar_name()
: QUERY::DbQuery
- set_tree_root()
: AP_main
, TreeNode
- set_tree_shader()
: AP_tree
- set_tree_style()
: AWT_graphic_tree
- set_type()
: awt_input_handler
, ED4_block
, POS_TREE1
, POS_TREE2
- set_under_construction()
: SEC_root
- set_update()
: ED4_base
- set_update_callback()
: AW_selection_list
- set_updist()
: NodeLeafDistance
- set_used()
: InfoWindow
- set_value()
: AW_selection_list_entry
, AW_selection_list_iterator
, awt_mask_awar_item
, awt_mask_item
, FINAL_TYPE< SEQTYPE >
- set_vector()
: Bitvector
- set_vertical_change_callback()
: AW_window
- set_vertical_font_overlap()
: AW_clipable
- set_vertical_scrollbar_position()
: AW_window
, AWT_canvas
- set_vertical_scrollbar_top_indent()
: AW_window
- set_visited()
: AP_tree_edge
- set_widget()
: VarUpdateInfo
- set_width()
: ED4_base
- set_window_title()
: AW_window
- set_window_title_intern()
: AW_window
- set_x_description()
: AP_userdef_matrix
- set_y_description()
: AP_userdef_matrix
- setAttachPoints()
: FINAL_TYPE< SEQTYPE >
- setBase()
: ST_base_vector
- setbit()
: Bitvector
, PART
- setBranchlen()
: FINAL_TYPE< SEQTYPE >
- SetColor()
: FINAL_TYPE< SEQTYPE >
- setComment()
: FieldTransfer::RuleSet
- setConditionalParameters()
: PrimerDesign
- setConstraints()
: SEC_constrainted
- setCursorTo()
: ED4_terminal
, FINAL_TYPE< SEQTYPE >
- setDotsAtEOSequence()
: AlignBuffer
- setDrawnSize()
: SEC_constrainted
- setDupCriteria()
: GroupSearch
- setError()
: QueryExpr
- setFalse()
: FINAL_TYPE< SEQTYPE >
, PS_BitMap
, PS_BitSet
- setFixpoint()
: FINAL_TYPE< SEQTYPE >
- setFixpoints()
: FINAL_TYPE< SEQTYPE >
- setHeadline()
: saiProbeData
- setKeeledState()
: TreeNode
- setLimits()
: GroupMatchScorer
- setLineNumber()
: LineReader
- setMappings()
: FINAL_TYPE< SEQTYPE >
- setMaxPoints()
: output
- setName()
: FINAL_TYPE< SEQTYPE >
, SEC_structure_toggler
- setNewerThan()
: timestamp
- setNewImport()
: ImportTestData
- setNewSearch()
: ED4_SearchResults
- setNull()
: SmartPtr< T, C >
- setNum()
: PS_Node
- setOlderThan()
: timestamp
- SetOnce()
: SetOnce
- SetOpenGLBackGroundColor()
: FINAL_TYPE< SEQTYPE >
- setParameters()
: ArbProbeCollection
, ArbProbeMatchWeighting
- setPerErrorPenalties()
: GroupMatchScorer
- setPosition()
: StringParser
- setPositionalParameters()
: PrimerDesign
- setProbeTarget()
: saiProbeData
- setRelativePenalties()
: GroupMatchScorer
- setScorer()
: SpecSetRegistry
- setSearchRange()
: GroupSearch
- setSpecies()
: SpeciesInTwoTrees
- setStandardSize()
: SEC_constrainted
- setSubtreeRoot()
: AP_subtree
- setTargetType()
: FieldTransfer::WriteRule
- setTo()
: ST_base_vector
- setTrue()
: FINAL_TYPE< SEQTYPE >
, PS_BitMap
, PS_BitSet
- setup()
: BaseFrequencies
- Setup()
: iupac::Setup
- setup()
: probe_statistic_struct
, probe_struct_global
- setup_changed_cb()
: AW_helix
, ItemFieldShader
- setup_test_postcondition()
: Globals
- setup_test_precondition()
: Globals
- setUserActionTracker()
: AW_root
- setValue()
: DecisionTree
- SetVariables()
: SetVariables
- setx()
: AW::Position
, AW::Vector
- sety()
: AW::Position
, AW::Vector
- shade()
: ItemFieldShader
, ItemShader
, ShaderPlugin
, TopologyShader
- shader_awar()
: FINAL_TYPE< SEQTYPE >
- shader_plugged_into()
: ShaderPlugin
- ShaderPlugin()
: ShaderPlugin
- shadow_width()
: AW_window
- shall_accept_missing_data()
: CLI
- shall_add_bootstraps()
: CLI
- shall_add_branch_length()
: CLI
- shall_add_group_names()
: CLI
- shall_be_pretty()
: CLI
- shall_delete_tree()
: CLI
- shall_edit()
: AliEditor
- shall_import_tree()
: CLI
- shall_replace_problem_chars()
: CLI
- shall_show_remark_for()
: BootstrapConfig
- shallCopyBefore()
: AdaptedAlignmentTransporter
, DontTransportAlignment
, FieldTransfer::AlignmentTransporter
- shallDisplayPosition()
: SEC_db_interface
, SEC_root
- shallTransferUndefFields()
: FieldTransfer::RuleSet
- shift()
: AP_STACK< ELEM >
, AW_zoomable
, NtreeCommandLine
- shift_op()
: shift_op
- short_inch()
: PaperFormat
- shouldHaveBeenKeeled()
: GroupPenalty
- show()
: AW_window
, AWT_graphic
, AWT_graphic_tree
- Show()
: ED4_base
, ED4_manager
, ED4_root_group_manager
, ED4_terminal
- show()
: FINAL_TYPE< SEQTYPE >
- Show()
: FINAL_TYPE< SEQTYPE >
- show()
: FINAL_TYPE< SEQTYPE >
- Show()
: FINAL_TYPE< SEQTYPE >
- show()
: GEN_graphic
, RNA3D_Graphics
, SAI_graphic
- show_clicked_cursor()
: ED4_cursor
- show_comment()
: arb_progress
, ArbProgress::nestable
- show_cursor_at()
: ED4_cursor
- show_for_index()
: PT_statistic
- show_help()
: CLI
- show_help_if_useful()
: CLI
- show_message()
: GroupChanges
- show_modal()
: AW_window
- show_ruler()
: AWT_graphic_tree
- show_warning()
: MessageSpamFilter
- show_warnings()
: Importer
- ShowCursor()
: ED4_cursor
- showFilenameInLineError()
: LineReader
- shown()
: Warnings
- shown_sequence_to_screen()
: ED4_remap
- shows_xpos()
: ED4_window
- sig_is_equal_to()
: TypedDatabaseCallback
- sigma_truncation()
: probe_combi_statistic
- simple()
: RootAsWindowCallback
- SimpleCmmd()
: FINAL_TYPE< SEQTYPE >
- SimpleFormatReader()
: SimpleFormatReader
- SimpleLocation()
: SimpleLocation
- SimpleRoot()
: SimpleRoot
- SimpleTester()
: SimpleTester
- SimpleTree()
: FINAL_TYPE< SEQTYPE >
- sin()
: AW::Angle
- single_in_generation()
: Generation
- singleTreeDistanceSum()
: Multiroot
- sink()
: Sonde
- size()
: ALI_TARRAY< T >
, arb_test::expectation_group
, AW_gc_manager
, AW_selection_list
, aw_xargs
, BaseFrequencies
, BI_helix
, cache::Cache< SMARTPTR >
, CharPtrArray
, chartable::SepBaseFreq
, Distributor
, ED4_list< T >
, EdgeChain
, FieldTransfer::RuleSet
, GBENTRY
, GBL_streams
, GroupCluster
, HelixAlignmentQuality
, Int< I >
, MarkerDisplay
, MarkerPosition
, MG_remaps
, Multiroot
, Oligo
, PartRegistry
, PosRange
, QueriedGroups
, RangeList
, RSpecSet
, symmetric_matrix< T >
, TSpecSet
- size2idx()
: MemBlockManager
- SizeAwarable()
: SizeAwarable
- SizeAwareRoot()
: SizeAwareRoot
- SizeAwareTree()
: FINAL_TYPE< SEQTYPE >
- sizeChanged()
: FINAL_TYPE< SEQTYPE >
, SEC_base
- SizedBufferPtr()
: SizedBufferPtr< T >
- SizedCstr()
: SizedCstr
- skipOverLinesThat()
: Reader
- SlaveCanvas()
: SlaveCanvas
- sleep()
: ARB_inc_sleep
- slice_down()
: AliData
, AliDataSlice
, FINAL_TYPE< SEQTYPE >
, LazyAliData
, TypedAliData< T >
- slow()
: AW_device
- smaller_extent()
: AW::Rectangle
- SmartPtr()
: SmartPtr< T, C >
- Smoother()
: Smoother
- softbase()
: softbase
- solution()
: ALI_PREALIGNER
- solutions()
: ALI_ALIGNER
- somehow()
: AW::FillStyle
- son()
: ARB_edge
- Sonde()
: Sonde
- Sondentopf()
: Sondentopf
- sonNode()
: AP_tree_edge
- sort()
: AW_selection_list
, CharPtrArray
, probe_combi_statistic
- sort_and_uniq()
: CharPtrArray
- sort_by()
: QueriedGroups
- sort_list_join()
: List< Type >
- sort_list_subtract()
: List< Type >
- sortByName()
: FINAL_TYPE< SEQTYPE >
- SortByTopo()
: SortByTopo
- SortClusterIDsBy()
: SortClusterIDsBy
- sortCustom()
: AW_selection_list
- SortedFreq()
: SortedFreq
- sotl_list()
: List< Type >
- source()
: ARB_edge
- source_element()
: DragNDrop
- SourceLineno()
: Link
- SpatialTuple()
: FINAL_TYPE< SEQTYPE >
- Spec()
: TreeAdmin::Spec
- special_window_refresh()
: ED4_root
- species()
: ClickedTarget
- species_count()
: TreeInfo
- SpeciesFlag()
: SpeciesFlag
- SpeciesInTwoTrees()
: SpeciesInTwoTrees
- speciesLabel()
: ACI_Labeler
, FINAL_TYPE< SEQTYPE >
, Node_ID_Labeler
, TreeLabeler
- SpeciesSelector()
: SpeciesSelector
- SpeciesSpace()
: SpeciesSpace
- specific_reset()
: AW_trackPositions_device
, AW_trackSpecies_device
- SpecificAliData()
: SpecificAliData< T >
- SpecificGap()
: SpecificGap< T >
- specifiesTrueChars()
: SaiBoolRule
- SpecSet()
: SpecSet
- SpecSetRegistry()
: SpecSetRegistry
- split()
: FINAL_TYPE< SEQTYPE >
- split_depth()
: Partition
- split_loop()
: SEC_root
- Splits()
: Splits
- spool()
: PrintMaybe
, SPOOLER
- SpoolableColor()
: SpoolableColor
- SpoolableString()
: SpoolableString
- SPOOLER()
: SPOOLER
- sprint()
: Item
- sprint_centigrade_list()
: PD_formatter
- SQ_add()
: SQ_GroupData
, SQ_GroupData_Impl< I >
- SQ_add_sequence()
: SQ_GroupData
, SQ_GroupData_RNA
- SQ_ambiguities()
: SQ_ambiguities
- SQ_calc_consensus()
: SQ_GroupData
, SQ_GroupData_RNA
- SQ_calc_helix_layout()
: SQ_helix
- SQ_calc_physical_layout()
: SQ_physical_layout
- SQ_count_ambiguities()
: SQ_ambiguities
- SQ_count_sequences()
: SQ_GroupData
- SQ_get_avg_bases()
: SQ_GroupData
- SQ_get_avg_gc()
: SQ_GroupData
- SQ_get_gc_proportion()
: SQ_physical_layout
- SQ_get_iupac_value()
: SQ_ambiguities
- SQ_get_no_helix()
: SQ_helix
- SQ_get_nr_ambiguities()
: SQ_ambiguities
- SQ_get_nr_sequences()
: SQ_GroupData
- SQ_get_number_of_bases()
: SQ_physical_layout
- SQ_get_percent_ambiguities()
: SQ_ambiguities
- SQ_get_strong_helix()
: SQ_helix
- SQ_get_weak_helix()
: SQ_helix
- SQ_GroupData()
: SQ_GroupData
- SQ_GroupData_Impl()
: SQ_GroupData_Impl< I >
- SQ_GroupData_RNA()
: SQ_GroupData_RNA
- SQ_helix()
: SQ_helix
- SQ_init_consensus()
: SQ_GroupData
, SQ_GroupData_Impl< I >
- SQ_is_initialized()
: SQ_GroupData
- SQ_physical_layout()
: SQ_physical_layout
- SQ_print_on_screen()
: SQ_GroupData
, SQ_GroupData_Impl< I >
- SQ_set_avg_bases()
: SQ_GroupData
- SQ_set_avg_gc()
: SQ_GroupData
- st_check_cb_data()
: st_check_cb_data
- ST_Container()
: ST_Container
- ST_ML()
: ST_ML
- ST_rate_matrix()
: ST_rate_matrix
- StackFrameData()
: StackFrameData
- standardize()
: AW::LineVector
, AW::Rectangle
, PART
- standardSize()
: SEC_constrainted
- start()
: AW::LineVector
, BufferPtr< T >
, PosRange
, References
- start_message()
: Location
- start_recording()
: MacroRecorder
- start_sorted_retrieval()
: DeconstructedTree
- startAttachAbspos()
: FINAL_TYPE< SEQTYPE >
- startAttachPoint()
: FINAL_TYPE< SEQTYPE >
- startLineCounter()
: BaseCounter
- StartPos()
: GEN_gene
- startpos()
: Scaler
- starts()
: ali_aligner_dellist
- startSaveAs()
: ArbDBWriter
- startsWithBlanks()
: startsWithBlanks
- StaticData()
: StaticData
- std_gap()
: TypedAliData< T >
- std_gap_ptr()
: TypedAliData< T >
- steps()
: PrefixIterator
- stop()
: RecordingMacro
- stop_recording()
: MacroRecorder
- StorableSelectionList()
: StorableSelectionList
- store()
: AngleBuffer
, AW_at_auto
, AW_at_maxsize
, AW_at_size
, AW_at_storage
- Store()
: AWT_configuration
- store()
: ClustersData
- Store2D3Dinfo()
: Structure3D
- Store2Dinfo()
: Structure3D
- store_all()
: ClustersData
- store_at_to()
: AW_window
- store_changed_field_content()
: AWT_configuration
- store_command_data()
: AWT_graphic_tree
- store_config()
: ItemFieldShader
, ShaderPlugin
, TopologyShader
- store_config_cb()
: FINAL_TYPE< SEQTYPE >
- store_pos()
: PS_FileBuffer
- store_positions_sorted()
: SlaveCanvas_internal
- Store_species()
: Store_species
- store_window()
: AliAdmin
- storeAllHelices()
: AngleBuffer
- storeBetterMatch()
: RSpecSet
- StoreCoordinates()
: Structure3D
- StoreCurrSpeciesDifference()
: Structure3D
- stored_costs()
: FINAL_TYPE< SEQTYPE >
- stored_external()
: gb_transaction_save
, GBENTRY
- stored_internal()
: GBENTRY
- storeDots()
: CompactedSequence
- StoreHelixNrInfo()
: Structure3D
- StoreInsertions()
: Structure3D
- str()
: arb_test::str
- strandAwayFrom()
: FINAL_TYPE< SEQTYPE >
- strandToOutside()
: FINAL_TYPE< SEQTYPE >
- strandToRoot()
: FINAL_TYPE< SEQTYPE >
- strandTowards()
: FINAL_TYPE< SEQTYPE >
- StrArray()
: FINAL_TYPE< SEQTYPE >
- strf()
: arb_test::StaticCode
- StrictlyAliased_BasePtrRef()
: StrictlyAliased_BasePtrRef< DERIVED, BASE >
- StrictlyTypedCallback()
: StrictlyTypedCallback< RT, P1, P2, P3 >
- string()
: ALI_NORM_SEQUENCE
, ALI_SEQUENCE
- String()
: Label
- StringParser()
: StringParser
- structure()
: SEC_db_interface
- Structure3D()
: Structure3D
- StrUniquifier()
: StrUniquifier
- sub()
: BaseFrequencies
, chartable::SepBaseFreq
- sub_and_add()
: BaseFrequencies
, chartable::SepBaseFreq
- sub_expected_children()
: probe_combi_statistic
- sub_life_counter()
: probe_combi_statistic
- sub_progress_skipped()
: arb_progress
- subexpr_count()
: RegExpr
- subexpr_match()
: RegExpr
- subset()
: Bitvector
- subtitle()
: arb_progress
- subtreeRoot()
: AP_subtree
- suffix()
: Oligo
- sum_child_lengths()
: TreeNode
- summarize()
: ST_base_vector
- summarize_all_ranges()
: LikelihoodRanges
- summarize_centigrade_hits()
: CentigradePos
- suppress()
: BackTraceInfo
, SuppressOutput
- suppress_update_and_refresh()
: AWT_auto_refresh
- SuppressOutput()
: SuppressOutput
- surface()
: AW::Rectangle
- swap()
: CharPtrArray
, DI_GLOBAL_MATRIX
, GBL_streams
, probe_combi_statistic
- swap_all()
: ClustersData
- swap_assymetric()
: FINAL_TYPE< SEQTYPE >
- swap_content()
: GBS_strstruct
- swap_node_info()
: TreeNode
- swap_son_layout()
: AP_tree_members
- swap_sons()
: AP_tree
, FINAL_TYPE< SEQTYPE >
, TreeNode
- switch_to()
: FunInfo
- symmetric_matrix()
: symmetric_matrix< T >
- SymmetricMatrixMapper()
: SymmetricMatrixMapper
- sync_DB_model_and_view()
: AWT_canvas