- a -

• abort() : Dragged , Reader
• abort_transaction() : GB_MAIN_TYPE
• aborted() : arb_progress , ArbProgress::nestable , InsertData
• abs() : AW_rgb_diff
• abs_2_rel() : BasePosition
• abs_count() : BasePosition
• AbsLoc() : AbsLoc
• accept() : AP_main , PARSIMONY_testenv< SEQTYPE >
• accept_all() : AP_main
• accept_if() : AP_main , PARSIMONY_testenv< SEQTYPE >
• accept_N_mismatches() : MatchRequest
• accept_proposed() : Cluster
• accept_resources() : NodeStack , StackFrameData
• acceptCurrentState() : FINAL_TYPE< SEQTYPE >
• accepted() : Mismatches
• access() : cache::CacheHandle< SMARTPTR >
• ACI_Labeler() : ACI_Labeler
• action() : remote_awars
• activate() : AW_window , ItemFieldShader , PlugIn , ShaderPlugin , TopologyShader
• activate_plugin() : FINAL_TYPE< SEQTYPE > , ItemShader
• activate_plugin_impl() : FINAL_TYPE< SEQTYPE >
• activateColorRange() : AW_gc_manager
• active() : ItemShader
• active_plugin_name() : FINAL_TYPE< SEQTYPE > , ItemShader
• active_range_changed_cb() : AW_gc_manager
• AdaptedAlignmentTransporter() : AdaptedAlignmentTransporter
• add() : Alignment , arb_test::expectation_group , ArbProbeCollection , AW_root_cblist , aw_xargs , AWT_config_definition , awt_input_mask_id_list , BaseCounts , BaseFrequencies , CallbackList< CB > , ChainEntryBuffer , chartable::SepBaseFreq , ClustersData , ColorMap , ConsensusTreeBuilder , count_mutpsite , count_nothing , count_unweighted , count_weighted , DiffLines , ExecutingMacro , FieldTransfer::RuleSet , FINAL_TYPE< SEQTYPE > , GroupSearchCommon , LikelihoodRanges , LineQueue , MetaInfo , NodeMarkers , OligoRegistry , PH_NEIGHBOUR_DIST , PrintMaybe , RangeList , Reference , References , RootSynchronizer , Sampler , Seq , Store_species , TreeAwarRegistry , TreeContainer , VarianceSampler
• add_attribute() : FINAL_TYPE< SEQTYPE >
• add_autoscroll() : SEC_root
• add_awar_callbacks() : awt_item_type_selector
• add_awarItem_callbacks() : awt_mask_awar_item
• add_callback() : AW_awar , AW_helix , TrackedFile
• add_candidate() : QueriedGroups
• add_cb() : ED4_cb_list< BASE, BASECB >
• add_color() : gc_range
• add_color_groups() : AW_gc_manager
• add_comment() : GcgWriter
• add_db_callbacks() : awt_linked_to_item
• add_dbid() : References
• add_delete_callback() : ED4_manager
• add_detach_area() : InfoWindow
• add_filters_to() : CLI
• add_gc() : AW_gc_manager , AW_GC_set
• add_gc_range() : AW_gc_manager
• add_global_id() : awt_input_mask_global
• add_handler() : FINAL_TYPE< SEQTYPE >
• add_help() : FINAL_TYPE< SEQTYPE >
• add_hierarchy_cb() : GB_MAIN_TYPE
• add_hit() : MatchRequest
• add_hits_for_children() : MatchRequest
• add_informed_group() : QueriedGroups
• add_line() : AW_xfig
• add_local_id() : awt_input_mask_global
• add_members_from() : PART
• add_name() : UniqueNameDetector
• add_parent_length() : TreeNode::LengthCollector
• add_planned_interruption() : MacroRecorder
• add_pos_changed_cb() : LocationEditor
• add_predefined_to() : AWT_configuration
• add_prefix() : FailedAt
• add_reader() : MultiFieldReader
• add_reference() : MG_remap
• add_relative() : LikelihoodRanges
• add_remark() : FINAL_TYPE< SEQTYPE >
• add_remarks_from() : FINAL_TYPE< SEQTYPE >
• add_SAI_filter() : FilteredExport
• add_sequence_changed_cb() : FINAL_TYPE< SEQTYPE >
• add_short() : NameInformation
• add_son() : FINAL_TYPE< SEQTYPE > , XML_Comment , XML_Node , XML_Text
• add_target_var() : AW_awar
• add_timed_callback() : AW_root
• add_timed_callback_never_disabled() : AW_root
• add_to_dimension() : ED4_folding_line
• add_to_highlighted() : ED4_root
• add_to_top_left_dimension() : ED4_scrolled_rectangle
• add_tracked_to() : ExportFieldTracker
• add_unchecked() : CallbackList< CB >
• add_warning() : TreeReader
• addChild() : PS_Candidate , PS_Node
• addComment() : FINAL_TYPE< SEQTYPE >
• addCount() : BaseCounter , UsedColor
• added() : DiffLines
• added_sequences() : BaseFrequencies
• addedHeadline() : ArbMatchResult
• addLine() : BaseCounter , SequenceBuffer
• addOperator() : FINAL_TYPE< SEQTYPE >
• addPenalty() : GroupPenalty
• addProbe() : PS_Node
• addProbes() : PS_Node
• addProbesInverted() : PS_Node
• addQualifiedEntry() : Feature
• addQueryExpression() : GroupSearch
• addRefToGene() : PosGene
• addResultSet() : ArbMatchResultsManager
• addRule() : SaiBoolchainOperator
• addSearchPosition() : ED4_SearchResults
• addSequence() : FINAL_TYPE< SEQTYPE > , MultiFastaWriter , Writer
• addSortCriterion() : GroupSearch
• addTranslation() : FINAL_TYPE< SEQTYPE >
• addWeightAndLength() : PART
• addXpair() : XString
• adjacent_screen_positions() : ED4_remap
• adjust_clipping_rectangle() : ED4_base
• advance() : StringParser
• after() : PosRange , timestamp
• Age() : AP_tree_edge
• aimTo() : TargetGroup , TargetItem
• AISC_Object() : AISC_Object
• akt_size() : ALI_TSTACK< T >
• ALI_ALIGNER() : ALI_ALIGNER
• ali_aligner_cell() : ali_aligner_cell
• ali_aligner_column() : ali_aligner_column
• ali_aligner_dellist() : ali_aligner_dellist
• ali_aligner_dellist_elem() : ali_aligner_dellist_elem
• ali_aligner_last_cell() : ali_aligner_last_cell
• ali_aligner_result() : ali_aligner_result
• ALI_ARBDB() : ALI_ARBDB
• ali_family_member() : ali_family_member
• ALI_MAP() : ALI_MAP
• ALI_NORM_SEQUENCE() : ALI_NORM_SEQUENCE
• ALI_PATHMAP() : ALI_PATHMAP
• ALI_PREALIGNER() : ALI_PREALIGNER
• ali_prealigner_approx_element() : ali_prealigner_approx_element
• ali_prealigner_approximation() : ali_prealigner_approximation
• ali_prealigner_cell() : ali_prealigner_cell
• ali_prealigner_column() : ali_prealigner_column
• ali_prealigner_mask() : ali_prealigner_mask
• ALI_PROFILE() : ALI_PROFILE
• ALI_PT() : ALI_PT
• ali_pt_member() : ali_pt_member
• ALI_selection() : ALI_selection
• ALI_sellst_spec() : ALI_sellst_spec
• ALI_SEQUENCE() : ALI_SEQUENCE
• ALI_SUB_SOLUTION() : ALI_SUB_SOLUTION
• ALI_TARRAY() : ALI_TARRAY< T >
• ALI_TLIST() : ALI_TLIST< T >
• ALI_TLIST_ELEM() : ALI_TLIST_ELEM< T >
• ALI_TSTACK() : ALI_TSTACK< T >
• AliAdmin() : AliAdmin
• AliApplicable() : AliApplicable
• AliChange() : AliChange
• AliCompositeCommand() : AliCompositeCommand
• AliData() : AliData
• AliDeleteCommand() : AliDeleteCommand
• AliEditor() : AliEditor
• AliEntryCounter() : AliEntryCounter
• AliFormatCommand() : FINAL_TYPE< SEQTYPE >
• align_helix_strands() : SEC_region
• align_to() : AlignmentReference , ConsensusReference , ExplicitReference , SearchRelativesReference
• AlignBuffer() : AlignBuffer
• AlignDataAccess() : AlignDataAccess
• aligned_awar() : AliAdmin
• aligned_name() : AliAdmin
• AlignedSequenceLoader() : FINAL_TYPE< SEQTYPE >
• Aligner() : Aligner
• alignInto() : LineQueue
• Alignment() : Alignment
• alignment_name() : MG_remaps
• alignment_too_short() : XString
• AlignmentReference() : AlignmentReference
• AliInsertCommand() : AliInsertCommand
• AliNameAndType() : AliNameAndType
• AliView() : AliView
• all() : arb_test::FINAL_TYPE< T > , TransTables
• all_are_selected() : ED4_multi_species_manager
• all_available_pops_will_produce_valid_trees() : PARSIMONY_testenv< SEQTYPE >
• all_available_reverts_will_produce_valid_trees() : AP_main
• all_closed() : AWT_graphic_tree_group_state
• all_marked_opened() : AWT_graphic_tree_group_state
• all_opened() : AWT_graphic_tree_group_state
• all_terminal_closed() : AWT_graphic_tree_group_state
• alloc_data() : GBENTRY
• alloc_mem() : PartitionSize
• alloc_named_data_color() : AW_window
• allocate_bitstring() : SpecSetRegistry
• allocate_detach_id() : InfoWindowRegistry
• allocated_index() : CharPtrArray
• allow() : TransTables
• allow_bottom_font_overlap() : AW_clipable
• allow_delete_window() : AW_window
• allow_left_font_overlap() : AW_clipable
• allow_lookup() : GroupCluster
• allow_right_font_overlap() : AW_clipable
• allow_title_reuse() : arb_progress , ArbProgress::nestable
• allow_top_font_overlap() : AW_clipable
• allowAll() : TransTables
• allowed_duration() : LimitedTime
• allowed_mismatches() : MatchRequest
• allowed_to_contain() : ED4_objspec
• allowedMismatches() : ArbProbe
• allTreesDeconstructed() : RootSynchronizer
• already_delivered() : Clusterer
• alreadyUsedNode() : PS_Candidate
• amountzero() : arb_test::group_match
• analyse() : PT_statistic
• analyse_distances() : AP_tree
• analyseDistances() : BranchWindow
• Analyser() : FINAL_TYPE< SEQTYPE >
• ancestor_common_with() : TreeNode
• Angle() : AW::Angle
• AngleBuffer() : AngleBuffer
• announce() : DisplayFormat , MostUsedPos , SEC_drawn_positions
• announce_added() : ED4_objspec
• announce_base_position() : SEC_root
• announce_current_species() : ED4_host , ED4_plugin_host
• announce_db_close() : gb_local_data
• announce_db_open() : gb_local_data
• announce_deletion() : ED4_base_position , ED4_cursor , ED4_root , ED4_window
• announce_exit_pc() : Location
• announce_result_list() : GroupUIdata
• announce_screen_update() : AWT_canvas
• announce_shader() : ShaderPlugin
• announce_source_database() : ExportFieldScanner
• announce_tree_constructed() : TreeNode
• announce_tree_select_list() : GroupUIdata
• announce_update() : MasterCanvas , ScrollSynchronizer
• announce_useraction_in() : ED4_root
• announce_viewport_size() : SlaveCanvas_internal
• announceGene() : GenePositionMap
• announceLoop() : PerfTimer
• any() : TransTables
• AP_combinableSeq() : AP_combinableSeq
• AP_DefaultTreeShader() : AP_DefaultTreeShader
• AP_filter() : AP_filter
• AP_main() : AP_main
• AP_matrix() : AP_matrix
• AP_pars_root() : FINAL_TYPE< SEQTYPE >
• AP_pos_var() : AP_pos_var
• AP_rates() : AP_rates
• AP_sequence() : AP_sequence
• AP_sequence_parsimony() : FINAL_TYPE< SEQTYPE >
• AP_sequence_protein() : FINAL_TYPE< SEQTYPE >
• AP_sequence_simple_protein() : AP_sequence_simple_protein
• AP_smatrix() : AP_smatrix
• AP_subtree() : AP_subtree
• AP_tree() : AP_tree
• AP_tree_edge() : AP_tree_edge
• AP_tree_nlen() : FINAL_TYPE< SEQTYPE >
• AP_tree_root() : AP_tree_root
• AP_TreeShader() : AP_TreeShader
• AP_userdef_matrix() : AP_userdef_matrix
• AP_weights() : AP_weights
• append() : Dots , FastAlignInsertion , FINAL_TYPE< SEQTYPE > , HeaderList , LooseBases , PartQueue , PS_Node , QueryExpr , Token , TokenList , TokenListBlock
• append_code() : Package
• append_elem() : ED4_list< T >
• append_end() : ALI_TLIST< T >
• append_front() : ALI_TLIST< T >
• append_linefeed() : Package
• append_member() : ED4_container
• append_to() : FINAL_TYPE< SEQTYPE >
• append_to_config_string() : GBT_config_item
• appID() : remote_awars
• applies() : CharPredicate
• apply() : AliAutoFormatCommand , AliCompositeCommand , AliDeleteCommand , AliEditCommand , AliInsertCommand , EditedTerminal , FINAL_TYPE< SEQTYPE > , SaiAciApplicator , SaiBoolchainOperator , SaiBoolRule , SaiOperator
• apply_aci_to_remarks() : TreeNode
• apply_config() : AW_GC
• apply_focus_policy() : AW_root
• apply_sensitivity() : AW_root
• apply_to_alignment() : AliApplicable
• apply_zoom_settings_for_treetype() : AWT_graphic_tree
• applyTo() : MatrixOrder
• approximation() : ALI_PREALIGNER
• arb_assert() : arb_test::StaticCode
• ARB_countedTree() : ARB_countedTree
• ARB_edge() : ARB_edge
• ARB_ERROR() : ARB_ERROR
• ARB_inc_sleep() : ARB_inc_sleep
• ARB_init_perl_interface() : ARB_init_perl_interface
• arb_prm_struct() : arb_prm_struct
• arb_progress() : arb_progress
• arb_r2a_pro_2_nuc() : arb_r2a_pro_2_nuc
• arb_r2a_pro_2_nucs() : arb_r2a_pro_2_nucs
• ARB_seqtree() : ARB_seqtree
• ARB_seqtree_root() : ARB_seqtree_root
• arb_suppress_progress() : arb_suppress_progress
• ARB_timeout() : ARB_timeout
• ARB_timestamp() : ARB_timestamp
• ARB_tree_info() : ARB_tree_info
• ARBDB_memory_manager() : ARBDB_memory_manager
• ArbDBWriter() : ArbDBWriter
• ArbImporter() : ArbImporter
• ArbMatchResult() : ArbMatchResult
• ArbMatchResultSet() : FINAL_TYPE< SEQTYPE >
• ArbMatchResultsManager() : ArbMatchResultsManager
• ArbParsimony() : ArbParsimony
• ArbPC_Context() : ArbPC_Context
• ArbPM_Context() : ArbPM_Context
• ArbProbe() : ArbProbe
• ArbProbeCollection() : ArbProbeCollection
• ArbProbeMatchWeighting() : ArbProbeMatchWeighting
• ArbRefCount() : ArbRefCount
• ArbStringCache() : ArbStringCache
• ArbTcpDat() : ArbTcpDat
• ArbWriteFile_Context() : ArbWriteFile_Context
• ArbWriter() : FINAL_TYPE< SEQTYPE >
• arc() : AW_device
• arg_type() : SelectedDatabase
• ArgCommand() : FINAL_TYPE< SEQTYPE >
• ArgParser() : ArgParser
• args_begin() : Prototype
• args_end() : Prototype
• argument_names_list() : Prototype
• artificial_hotkey() : awt_hotkeys
• as_container() : GBDATA
• as_entry() : GBDATA
• as_result_param() : AISC_Object
• as_string() : ComplementLocation , JoinedLocation , Location , Ostring , SimpleLocation
• ascii() : AW_rgb16
• assert_is_valid() : Validity
• assertChild() : PS_Node
• asserter() : arb_test::asserter
• assign() : arb_test::str , AW_clicked_box , AW_clicked_element , AW_clicked_line , AW_clicked_text , cache::CacheHandle< SMARTPTR > , FINAL_TYPE< SEQTYPE > , Output , SmartPtr< T, C > , UsedColor
• assign_stdout() : Output
• assign_to_widget() : aw_xargs
• assignToKey() : Dict
• at() : AW_window , ChainIteratorStage1 , ChainIteratorStage2 , Interpreter , Oligo , StringParser
• at_attach() : AW_window
• at_attach_to() : AW_window
• at_ifdef() : AW_window
• at_newline() : AW_window
• at_node() : Group
• at_ptr() : SpecificAliData< T > , SpecificGap< T > , TypedAliData< T >
• at_root() : TreeNode
• at_screen_update_call() : TREE_canvas
• at_shift() : AW_window
• at_unattach() : AW_window
• at_x() : AW_window
• at_y() : AW_window
• atEnd() : StringParser
• atleast() : arb_test::FINAL_TYPE< T >
• atmost() : arb_test::FINAL_TYPE< T >
• attach_selected_item() : InfoWindow
• attach_warning() : MessageAttachable
• attached_message() : MessageAttachable
• AttributeParser() : AttributeParser
• authAck() : remote_awars
• authReq() : remote_awars
• auto_awar() : AliAdmin
• auto_delete_array_ptr() : auto_delete_array_ptr< T >
• auto_delete_ptr() : auto_delete_ptr< T >
• auto_free_ptr() : auto_free_ptr< T >
• auto_increment() : AW_window
• auto_name() : AliAdmin
• auto_space() : AW_window
• auto_subtitles() : arb_progress , ArbProgress::counter , ArbProgress::nestable , FINAL_TYPE< SEQTYPE > , null_counter
• auto_unfold() : AWT_graphic_tree
• auto_update() : ScrollSynchronizer
• autocorrect_type() : ED4_block
• automark_awar() : BranchWindow
• AutoMatchSettings() : AutoMatchSettings
• autorun_macro() : NtreeCommandLine
• available() : LimitedTime
• avoid_warning() : ED4_WinContextFree
• AW_area_management() : AW_area_management
• AW_at() : AW_at
• AW_at_auto() : AW_at_auto
• AW_at_maxsize() : AW_at_maxsize
• AW_at_size() : AW_at_size
• AW_awar() : AW_awar
• AW_buttons_struct() : AW_buttons_struct
• AW_cb() : AW_cb
• AW_click_cd() : AW_click_cd
• AW_clicked_element() : AW_clicked_element
• AW_clicked_polygon() : FINAL_TYPE< SEQTYPE >
• AW_clipable() : AW_clipable
• AW_common() : AW_common
• AW_common_Xm() : AW_common_Xm
• AW_DB_selection() : AW_DB_selection
• AW_device() : AW_device
• AW_device_click() : FINAL_TYPE< SEQTYPE >
• AW_device_print() : FINAL_TYPE< SEQTYPE >
• AW_device_size() : AW_device_size
• AW_device_Xm() : FINAL_TYPE< SEQTYPE >
• AW_event() : AW_event
• AW_font_limits() : AW_font_limits
• AW_GC() : AW_GC
• AW_GC_config() : AW_GC_config
• AW_gc_manager() : AW_gc_manager
• AW_GC_set() : AW_GC_set
• AW_GC_Xm() : AW_GC_Xm
• AW_helix() : AW_helix
• AW_hsv() : AW_hsv
• AW_option_menu_struct() : AW_option_menu_struct
• AW_repeated_question() : FINAL_TYPE< SEQTYPE >
• AW_rgb16() : AW_rgb16
• AW_rgb_diff() : AW_rgb_diff
• AW_rgb_normalized() : AW_rgb_normalized
• AW_root() : AW_root
• AW_root_Motif() : AW_root_Motif
• AW_scalar() : AW_scalar
• AW_ScalerTransformer() : AW_ScalerTransformer
• AW_selection() : AW_selection
• AW_selection_list() : AW_selection_list
• AW_selection_list_entry() : AW_selection_list_entry
• AW_selection_list_iterator() : AW_selection_list_iterator
• AW_simple_device() : AW_simple_device
• AW_size_tracker() : AW_size_tracker
• AW_stylable() : AW_stylable
• AW_subset_selection() : AW_subset_selection
• AW_toggle_field_struct() : AW_toggle_field_struct
• AW_trackPositions_device() : AW_trackPositions_device
• AW_trackSpecies_device() : AW_trackSpecies_device
• AW_var_target() : AW_var_target
• AW_widget_refresh_cb() : AW_widget_refresh_cb
• AW_widget_value_pair() : AW_widget_value_pair
• AW_window() : AW_window
• AW_window_menu() : AW_window_menu
• AW_window_menu_modes() : AW_window_menu_modes
• AW_window_menu_modes_opengl() : AW_window_menu_modes_opengl
• AW_window_message() : AW_window_message
• AW_window_Motif() : AW_window_Motif
• AW_window_simple() : FINAL_TYPE< SEQTYPE >
• AW_window_simple_menu() : AW_window_simple_menu
• aw_xargs() : aw_xargs
• AW_xfig() : AW_xfig
• AW_zoomable() : AW_zoomable
• awar() : AW_root , awt_mask_awar_item , remote_awars
• awar2db() : awt_check_box , awt_numeric_input_field , awt_radio_button , awt_string_handler
• awar2scaler() : AW_ScalerTransformer
• awar_changed() : awt_mask_awar_item , awt_string_handler , awt_text_viewport , awt_variable , FINAL_TYPE< SEQTYPE >
• awar_charp_value() : LocationEditor
• awar_float() : AW_root
• awar_int() : AW_root
• awar_name() : awt_mask_awar_item
• awar_no_error() : AW_root
• awar_pointer() : AW_root
• awar_string() : AW_root
• awarname_active_range() : AW_gc_manager
• awroot() : SEC_db_interface
• awt_assignment() : awt_assignment
• AWT_auto_refresh() : AWT_auto_refresh
• AWT_canvas() : AWT_canvas
• awt_check_box() : awt_check_box
• AWT_config() : AWT_config
• AWT_config_definition() : AWT_config_definition
• AWT_configuration() : AWT_configuration
• AWT_configuration_selection() : AWT_configuration_selection
• AWT_distance_meter() : AWT_distance_meter
• AWT_graphic() : AWT_graphic
• AWT_graphic_event() : AWT_graphic_event
• AWT_graphic_parsimony() : AWT_graphic_parsimony
• AWT_graphic_tree() : AWT_graphic_tree
• AWT_graphic_tree_group_state() : AWT_graphic_tree_group_state
• awt_hotkeys() : awt_hotkeys
• awt_input_field() : awt_input_field
• awt_input_handler() : awt_input_handler
• awt_input_mask() : FINAL_TYPE< SEQTYPE >
• awt_input_mask_descriptor() : FINAL_TYPE< SEQTYPE >
• awt_input_mask_global() : awt_input_mask_global
• awt_input_mask_id_list() : awt_input_mask_id_list
• awt_item_type_selector() : awt_item_type_selector
• awt_linked_to_item() : awt_linked_to_item
• awt_marked_checkbox() : FINAL_TYPE< SEQTYPE >
• awt_mask_action() : awt_mask_action
• awt_mask_awar_item() : awt_mask_awar_item
• awt_mask_item() : awt_mask_item
• AWT_nonDB_graphic() : AWT_nonDB_graphic
• awt_numeric_input_field() : awt_numeric_input_field
• awt_radio_button() : awt_radio_button
• AWT_registered_itemtype() : AWT_registered_itemtype
• awt_script() : FINAL_TYPE< SEQTYPE >
• awt_script_viewport() : FINAL_TYPE< SEQTYPE >
• awt_string_handler() : awt_string_handler
• awt_text_viewport() : awt_text_viewport
• AWT_translator() : AWT_translator
• AWT_tree_selection() : AWT_tree_selection
• awt_variable() : awt_variable
• awt_viewport() : awt_viewport
• AwtiExportWriter() : FINAL_TYPE< SEQTYPE >