Here is a list of all class members with links to the classes they belong to:

- s -

• s : AW_awar , AW_hsv , AW_scalar , ReadSeqVars
• S2str() : AWT_translator
• S2strArray() : AWT_translator
• safe_remove() : CharPtrArray
• sai : common_filter_params
• SAI_graphic() : SAI_graphic
• sai_middle : SAI_string_builder
• 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 >
• same_line : gc_desc
• sameObject() : SmartPtr< T, C >
• Sampler() : Sampler
• save() : AW_selection_list
• Save() : AWT_configuration
• save() : ComplementLocation , DI_MATRIX , FileContent , FINAL_TYPE< SEQTYPE > , GBT_config , GfileFormat , 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
• saved_flags : gb_flag_types
• saved_x : AW_at , RNA3D_Global
• saved_xoff_for_label : AW_at
• saved_y : RNA3D_Global
• 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
• sc : ARB_TIME , TimeStamp
• scale : parameters , probe_combi_statistic , RNA3D_Global
• scale_branchlengths() : TreeNode
• scale_factor : parameters
• scaled_remark_ascend : BootstrapConfig
• Scaler() : Scaler
• scaler2awar() : AW_ScalerTransformer
• scaling() : Scaler
• scan() : parameters
• scan_display_widths() : Cluster
• scan_value_range_cb() : ItemFieldShader
• scanFields() : AvailableFieldScanner , ExportFieldScanner , ImportFieldScanner , MergeFieldScanner
• scanner : scan_db_insert
• score : island , score
• screen_depth : AW_root_Motif
• screen_rel : cursorpos
• screen_to_sequence() : ED4_remap
• ScreenToWinCoordinates() : FINAL_TYPE< SEQTYPE >
• screenXmax : FINAL_TYPE< SEQTYPE >
• screenYmax : FINAL_TYPE< SEQTYPE >
• scroll() : AWT_canvas , ED4_scroll_picture , ED4_scrolled_rectangle
• scroll_bar_horizontal : AW_window_Motif
• scroll_bar_vertical : AW_window_Motif
• scroll_cells() : MatrixDisplay
• scroll_into_view() : ED4_terminal
• scroll_links : ED4_root
• scroll_picture : ED4_root
• scroll_rectangle() : ED4_window
• scrollbars_and_scrolledRect_inSync() : ED4_window
• scrolled_rect : 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_system_folder : gb_local_data
• search_target_species() : ED4_container
• search_type : known_enum
• 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 : FINAL_TYPE< SEQTYPE >
• 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_delete : gb_flag_types
• security_level : GB_MAIN_TYPE
• security_name() : AliAdmin
• security_read : gb_flag_types
• security_write : gb_flag_types
• seen() : LimitTracker< T >
• seen_keeled : ColumnWidths
• seen_species : link_tree_data
• seenDups() : ID_checker
• select_all() : ED4_multi_species_manager
• select_awar() : AliAdmin
• select_bit : QUERY::DbQuery , QUERY::query_spec
• select_default() : AW_selection_list
• select_element_at() : AW_selection_list
• select_first() : SpeciesSelector
• select_group() : AWT_graphic_tree
• select_list_widget : AW_selection_list
• select_mode() : AW_window
• select_name() : AliAdmin
• select_next() : SpeciesSelector
• selected_mode : AW_window_Motif
• selected_plugin_changed_cb() : FINAL_TYPE< SEQTYPE >
• selected_probes : awar_vars
• selected_range_changed_cb() : FINAL_TYPE< SEQTYPE >
• selected_species_mark() : ED4_multi_species_manager
• SelectedDatabase() : SelectedDatabase
• selection_id : ArbPC_Context , ProbeMatchEventParam
• selection_list : AW_root_Motif
• selection_list_rescan_cb : MutableItemSelector
• SelectionListSpec() : SelectionListSpec
• selector : MutableBoundItemSel , QUERY::DbQuery
• 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
• sep_filter : IRS_data
• SepBaseFreq() : chartable::SepBaseFreq
• seq : cursorpos , hasSequence , Parser , ReadSeqVars
• Seq() : Seq
• seq_2_helix() : AW_helix
• seq_done() : FileWriter
• seq_gaps : SearchAwarList
• seq_name : NA_Sequence
• seqabbr : FINAL_TYPE< SEQTYPE >
• seqid : ReadSeqVars
• seqinf : RDP_comments
• SeqInfo() : SeqInfo
• seqlen : NA_Sequence , ReadSeqVars
• seqlencount : ReadSeqVars
• seqmaxlen : NA_Sequence
• SeqPart() : SeqPart
• seqtype : GmenuItem
• sequence : ali_family_member , ALI_MAP , ALI_NORM_SEQUENCE , ALI_PREALIGNER , ALI_PROFILE , ALI_SEQUENCE , apd_sequence , ArbProbe , DI_ENTRY , ED4_reference_terminals , FastSearchOccurrence , FastSearchSequence , NA_Sequence , NodeState
• SEQUENCE : Params
• sequence : Params , ProbeOccurrence , SEC_seq_data , SequencePosition
• sequence2base_position() : ED4_cursor
• sequence_change() : MostLikelySeq
• sequence_colors : ED4_root
• 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
• sequenceaci : import_format
• SequenceAliData() : SequenceAliData
• SequenceBuffer() : SequenceBuffer
• sequencecolumn : import_format
• sequenceend : import_format
• SequenceHandler() : SequenceHandler
• SequenceIterator() : SequenceIterator
• SequencePosition() : SequencePosition
• sequences_checked : dot_insert_stat
• sequencesrt : import_format
• sequencestart : import_format
• seqwidth : prettyopts
• server_communication : AN_gl_struct
• server_data : GB_MAIN_TYPE
• server_id : gbcms_create , GBDATA
• server_name : AN_gl_struct , probe_struct_global
• SERVERID : Params
• servername : ALI_PT_CONTEXT
• serverNumber : ProbeMatchSettings
• set() : AISC_Object , ALI_MAP , ALI_PATHMAP , ALI_TARRAY< T > , AlignBuffer , AP_matrix , AP_sequence , AW::Vector , DefinedCommands
• Set() : ED4_species_pointer , FINAL_TYPE< SEQTYPE >
• set() : FINAL_TYPE< SEQTYPE > , 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 : arb_status_implementation , 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 : SpecSet
• 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 : arb_status_implementation , 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_title : arb_status_implementation
• 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
• setvar : import_match
• SetVariables() : SetVariables
• setx() : AW::Position , AW::Vector
• sety() : AW::Position , AW::Vector
• shade() : ItemFieldShader , ItemShader , ShaderPlugin , TopologyShader
• shade_species : AP_TreeShader
• SHADED : AW::FillStyle
• SHADED_WITH_BORDER : AW::FillStyle
• ShadedValue : ValueTuple
• shader_awar() : FINAL_TYPE< SEQTYPE >
• shader_plugged_into() : ShaderPlugin
• ShaderPlugin() : ShaderPlugin
• shadow_thickness : AW_at
• 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
• shell : AW_window_Motif
• shift() : AP_STACK< ELEM > , AW_zoomable , NtreeCommandLine
• shift_op() : shift_op
• shift_x_to_fit : AWT_canvas
• shift_y_to_fit : AWT_canvas
• short_inch() : PaperFormat
• short_name : NA_Sequence
• short_node : probe_statistic_struct
• shorts : probe_statistic_struct
• shorts2 : probe_statistic_struct
• shortTable : chartable::SepBaseFreq
• should_be_indexed : gb_flag_types2
• shouldHaveBeenKeeled() : GroupPenalty
• show() : AW_window , AWT_graphic , AWT_graphic_tree
• Show() : ED4_base , ED4_manager , ED4_root_group_manager , ED4_terminal , FINAL_TYPE< SEQTYPE >
• show() : FINAL_TYPE< SEQTYPE > , GEN_graphic , RNA3D_Graphics , SAI_graphic , SearchAwarList
• show_100_if_empty : BootstrapConfig
• show_bonds : SEC_displayParams
• show_boots : BootstrapConfig
• show_circle : BootstrapConfig
• show_clicked_cursor() : ED4_cursor
• show_comment() : arb_progress , ArbProgress::nestable
• show_curpos : SEC_displayParams
• show_cursor_at() : ED4_cursor
• show_ecoli : format_props
• show_ecoli_pos : SEC_displayParams
• show_error : arb_handlers
• show_for_index() : PT_statistic
• show_gpos : format_props
• show_helixNrs : SEC_displayParams
• show_help() : CLI
• show_help_if_useful() : CLI
• show_message : arb_handlers , GroupChanges
• show_mismatches : format_props
• show_modal() : AW_window
• show_range_overlay : AW_gc_manager
• show_ruler() : AWT_graphic_tree
• show_strSkeleton : SEC_displayParams
• show_warning : arb_handlers , MessageSpamFilter
• show_warnings : arb_test::locinfo , Importer
• ShowCursor() : ED4_cursor
• showFilenameInLineError() : LineReader
• showGapsMessages : AlignParams
• shown() : Warnings
• shown_sequence_to_screen() : ED4_remap
• shows_xpos() : ED4_window
• sig_is_equal_to() : TypedDatabaseCallback
• sigma_truncation() : probe_combi_statistic
• Signature : Callback_FFV< RT, F1, F2 > , Callback_FVV< RT, FIXED > , Callback_VV< RT >
• SigP0F12 : Callback_FVF< RT, F1, F2 >
• SigP0F2 : Callback_FVF< RT, F1, F2 >
• SigP1 : Callback_FVF< RT, F1, F2 >
• simple() : RootAsWindowCallback
• SimpleCmmd() : FINAL_TYPE< SEQTYPE >
• SimpleFormatReader() : SimpleFormatReader
• SimpleLocation() : SimpleLocation
• SimpleRoot : FINAL_TYPE< SEQTYPE > , SimpleRoot
• SimpleTester() : SimpleTester
• SimpleTree() : FINAL_TYPE< SEQTYPE >
• sin() : AW::Angle
• single : DictTree
• single_in_generation() : Generation
• single_node : probe_statistic_struct
• single_pro : arb_r2a_pro_2_nuc
• singlemismatches : awar_vars
• SINGLETON : AW_root , TreeAwarRegistry
• singleTreeDistanceSum() : Multiroot
• sink() : Sonde
• sites : count_mutpsite
• size : aisc_bytes_list , aisc_static_set_mem , ALI_TARRAY< T > , arb_test::expectation_group , AW_gc_manager , AW_selection_list , aw_xargs , BaseFrequencies , BI_helix , bytestring , cache::Cache< SMARTPTR > , CharPtrArray , chartable::SepBaseFreq , DictData , Distributor , ED4_extension , ED4_list< T > , EdgeChain , FieldTransfer::RuleSet , FoundGroup , gb_buffer , gb_data_list , gb_extern_data2 , gb_extern_data , GB_HASH , GB_INTern_strings2 , GB_INTern_strings , GB_NUMHASH , gbb_Cluster , gbb_data , GBENTRY , GBL_streams , gbm_pool , GroupCluster , HelixAlignmentQuality , Int< I > , MarkerDisplay , MarkerPosition , MG_remaps , Multiroot , Oligo , PartRegistry , PosRange , PT_statistic::chain_head_mem , QueriedGroups , RangeList , RSpecSet , SQ_GroupData , symmetric_matrix< T > , TSpecSet , xfont
• size2idx() : MemBlockManager
• size_x : AW_xfig
• size_y : AW_xfig
• SizeAwarable() : SizeAwarable
• SizeAwareRoot : FINAL_TYPE< SEQTYPE > , SizeAwareRoot
• SizeAwareTree() : FINAL_TYPE< SEQTYPE >
• sizeChanged() : FINAL_TYPE< SEQTYPE > , SEC_base
• SizedBufferPtr() : SizedBufferPtr< T >
• SizedCstr() : SizedCstr
• sizeof_data : gb_cache_entry
• sizeof_this : g_b_undo_entry , g_b_undo_header , g_b_undo_list
• sizeofkeys : GB_MAIN_TYPE
• skeleton_thickness : SEC_displayParams
• skip_empty_tags : FINAL_TYPE< SEQTYPE >
• skipOverLinesThat() : Reader
• skipped : GroupChanges
• SlaveCanvas() : SlaveCanvas
• sleep() : ARB_inc_sleep
• slice_down() : AliData , AliDataSlice , FINAL_TYPE< SEQTYPE > , LazyAliData , TypedAliData< T >
• slider_pos_horizontal : AW_window , ED4_window
• slider_pos_vertical : AW_window , ED4_window
• slow() : AW_device
• smaller_extent() : AW::Rectangle
• SmartPtr() : SmartPtr< T, C >
• SmartPtr< T, Counted< T, AP > > : Counted< T, AP >
• smoothed : tree
• Smoother() : Smoother
• soci : gb_server_data , Hs_struct
• socket : aisc_com , gbcmc_comm , Socinf
• softbase() : softbase
• SOLID : AW::FillStyle
• solution() : ALI_PREALIGNER
• solutions() : ALI_ALIGNER
• somehow() : AW::FillStyle
• son() : ARB_edge , FullDictTree , gb_compress_list , gb_compress_tree , SingleDictTree
• son_list : NT_NODE
• Sonde() : Sonde
• Sondennamen : ST_Container
• Sondentopf() : Sondentopf
• sondentopf : ST_Container
• sonNode() : AP_tree_edge
• sons : FINAL_TYPE< SEQTYPE >
• sort() : AW_selection_list , CharPtrArray , probe_combi_statistic
• sort_and_uniq() : CharPtrArray
• sort_by : probe_struct_global , QueriedGroups
• sort_list_join() : List< Type >
• sort_list_subtract() : List< Type >
• sort_mask : QUERY::DbQuery
• sortBy : ProbeMatchSettings
• sortByName() : FINAL_TYPE< SEQTYPE >
• SortByTopo() : SortByTopo
• SortClusterIDsBy() : SortClusterIDsBy
• sortCustom() : AW_selection_list
• SortedFreq() : SortedFreq
• sotl_list() : List< Type >
• source() : ARB_edge , arb_prm_struct , Code , FINAL_TYPE< SEQTYPE > , g_b_undo_entry , OrgInfo
• source_element() : DragNDrop
• SourceLineno() : Link
• sp : ReadSeqVars
• sp_count : arb_prm_struct
• spacer : prettyopts
• SpatialTuple() : FINAL_TYPE< SEQTYPE >
• spec : ED4_base , gb_callback , gb_triggered_callback
• Spec() : TreeAdmin::Spec
• special_window_refresh() : ED4_root
• species() : ClickedTarget , common_filter_params , SpeciesConcatenateList , SpeciesMergeList
• species_count() : TreeInfo
• species_hash : link_tree_data
• species_mode : ED4_root
• species_name : ALI_GLOBAL , arb_params , ED4_abstract_sequence_terminal , QUERY::DbQuery , QUERY::query_spec , SpeciesConcatenateList , SpeciesMergeList
• species_sellist : ImportTestData
• species_timer : AP_tree_root
• 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
• speed : ArbProgress::nestable
• split() : FINAL_TYPE< SEQTYPE > , ProbeCommonSettings
• split_depth() : Partition
• split_loop() : SEC_root
• splits : PT_statistic
• Splits() : Splits
• spool() : PrintMaybe , SPOOLER
• SpoolableColor() : SpoolableColor
• SpoolableString() : SpoolableString
• SPOOLER : FINAL_TYPE< SEQTYPE > , SPOOLER
• spread : AP_tree_members
• 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
• src : merge_scheme
• srt : AW_awar , import_match
• st_check_cb_data() : st_check_cb_data
• ST_Container() : ST_Container
• ST_Liste : ST_Container
• st_ml : ED4_root
• ST_ML() : ST_ML
• st_ml_node : ED4_sequence_terminal
• ST_rate_matrix() : ST_rate_matrix
• stack : g_b_undo_header
• StackFrameData() : StackFrameData
• StackFrameData::destroyNode : FINAL_TYPE< SEQTYPE >
• StackFrameData::makeEdge : AP_tree_edge
• stamp : parameters
• standard : GenbankRef
• standardize() : AW::LineVector , AW::Rectangle , PART
• standardSize() : SEC_constrainted
• start : ali_aligner_dellist_elem , ali_pathmap_up_pointer , AW::LineVector , BufferPtr< T > , KL_Settings , PosRange , References , tree
• start_column : column
• start_message() : Location
• start_pos : GEN_position , Item
• start_recording() : MacroRecorder
• start_sorted_retrieval() : DeconstructedTree
• start_uncertain : GEN_position
• startAttachAbspos() : FINAL_TYPE< SEQTYPE >
• startAttachPoint() : FINAL_TYPE< SEQTYPE >
• startLineCounter() : BaseCounter
• StartPos() : GEN_gene
• startpos() : Scaler
• starts : ali_aligner_cell , ali_aligner_dellist
• startSaveAs() : ArbDBWriter
• startStop : AWT_Codon_Code_Definition
• startsWithBlanks() : startsWithBlanks
• stat : probe_struct_global
• stat_cons : ColumnQualityInfo
• stat_five : ColumnQualityInfo
• stat_half : ColumnQualityInfo
• stat_user : ColumnQualityInfo
• state : Parser
• Static : KL_Settings
• static_prop : ED4_objspec
• StaticData() : StaticData
• status : arb_handlers
• status_initialized : aw_stg_struct
• std_gap() : TypedAliData< T >
• std_gap_ptr() : TypedAliData< T >
• stencilSize : GLwDrawingAreaPart
• step_y : IRS_data
• steps() : PrefixIterator
• stereo : GLwDrawingAreaPart
• stop() : RecordingMacro
• stop_pos : GEN_position
• stop_recording() : MacroRecorder
• stop_uncertain : GEN_position
• stopAtFoldedGroups : KL_params
• 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 , CharPtrArray , Code
• strain : FINAL_TYPE< SEQTYPE >
• strandAwayFrom() : FINAL_TYPE< SEQTYPE >
• strandToOutside() : FINAL_TYPE< SEQTYPE >
• strandToRoot() : FINAL_TYPE< SEQTYPE >
• strandTowards() : FINAL_TYPE< SEQTYPE >
• StrArray() : FINAL_TYPE< SEQTYPE >
• strCen : Structure3D
• strf() : arb_test::StaticCode
• StrictlyAliased_BasePtrRef() : StrictlyAliased_BasePtrRef< DERIVED, BASE >
• StrictlyTypedCallback() : StrictlyTypedCallback< RT, P1, P2, P3 >
• string() : ALI_NORM_SEQUENCE , ALI_SEQUENCE , ED4_work_info
• String() : Label
• string : Word
• StringParser() : StringParser
• structure() : SEC_db_interface
• Structure3D() : Structure3D
• StrUniquifier() : StrUniquifier
• Style : AW::FillStyle
• style : AW_GC_config , BootstrapConfig
• sub() : BaseFrequencies , chartable::SepBaseFreq , Token
• 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
• subspecies : FINAL_TYPE< SEQTYPE >
• substitute_matrix : ALI_PROFILE_CONTEXT
• subtitle() : arb_progress
• subtreeRoot() : AP_subtree
• suffix : export_format , Oligo , SEQIO::ExportFormatInfo
• sum : count_unweighted , count_weighted
• sum_bonds : dt_bondssum
• sum_child_lengths() : TreeNode
• sum_data_size : gb_cache
• 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
• switchtext : TypeSwitch
• symbol : GfileFormat , GmenuItemArg
• symmetric_matrix() : symmetric_matrix< T >
• SymmetricMatrixMapper() : SymmetricMatrixMapper
• sync_DB_model_and_view() : AWT_canvas
• system : export_format , import_format