- i -
- icompare()
: TextRef
- ID_checker()
: ID_checker
- idAtPos()
: ClustersData
- idx2size()
: MemBlockManager
- if()
: arb_test::locinfo
- ignore()
: Xfig_Eater
- ignore_me()
: BaseFrequencies
- ignore_rest_of_file()
: FormatReader
, MackeReader
, Reader
, SimpleFormatReader
- ignore_unknown_refs()
: RefEntries::RefSelector
- implicit_inc()
: ArbProgress::counter
, FINAL_TYPE< SEQTYPE >
, null_counter
- import()
: Importer
- import_and_continueOnSuccess()
: ArbImporter
- import_data()
: ArbImporter
- import_format()
: import_format
- import_match()
: import_match
- import_section()
: Importer
- Importer()
: Importer
- ImportFieldScanner()
: ImportFieldScanner
- ImportSession()
: ImportSession
- ImportTestData()
: ImportTestData
- in_border()
: ED4_base
- in_consensus_terminal()
: ED4_cursor
- in_other_branch_than()
: TreeNode
- in_SAI_terminal()
: ED4_cursor
- in_same_branch_as()
: TreeNode
- in_shell()
: GB_shell
- in_single_mode()
: export_sequence_data
- in_species_seq_terminal()
: ED4_cursor
- inc()
: arb_progress
, ArbProgress::counter
, ArbProgress::nestable
, BufferPtr< T >
, FINAL_TYPE< SEQTYPE >
, HitCounter
, InsertData
, no_counter
, null_counter
, UsedColor
- inc_and_check_user_abort()
: arb_progress
- inc_and_error_if_aborted()
: arb_progress
- inc_by()
: arb_progress
, ArbProgress::counter
, ArbProgress::nestable
, FINAL_TYPE< SEQTYPE >
, null_counter
- inc_change()
: gb_header_flags
- inc_combine_count()
: AP_combinableSeq
- inc_hit_flag()
: Bakt_Info
- inc_long()
: chartable::SepBaseFreq
- inc_short()
: chartable::SepBaseFreq
- inc_to()
: arb_progress
, ArbProgress::counter
, ArbProgress::nestable
, FINAL_TYPE< SEQTYPE >
, null_counter
- inc_to_avoid_overflow()
: arb_progress
, ArbProgress::counter
, ArbProgress::nestable
, FINAL_TYPE< SEQTYPE >
, null_counter
- includes()
: Range
- incMarker()
: NodeMarkers
- incNodeSize()
: NodeMarkers
- increase()
: LimitedTime
- increaseBy()
: ST_base_vector
- increment_at_commands()
: AW_window
- indent()
: indent
, output
- Indent()
: XML_Node
- independent_distribution()
: TreeNode::LengthCollector
- index()
: ArbMatchResult
, FINAL_TYPE< SEQTYPE >
, PART
- index2bitset()
: AWT_translator
- index2spro()
: AWT_translator
- index_check_in()
: GBENTRY
- index_check_out()
: GBENTRY
- index_of()
: CharPtrArray
, KeySorter
- index_re_check_in()
: GBENTRY
- indexOf()
: AP_tree_edge
, FINAL_TYPE< SEQTYPE >
- indicate_selected()
: AW_clicked_box
, AW_clicked_element
, AW_clicked_line
, AW_clicked_text
, FINAL_TYPE< SEQTYPE >
- inform_about_delete()
: AP_tree_root
- inform_group()
: Candidate
- InfoWindow()
: InfoWindow
- init()
: AISC_Object
, ALI_GLOBAL
, AP_DefaultTreeShader
, AP_rates
, AP_TreeShader
, AW_window_menu
, AW_window_menu_modes
, AW_window_menu_modes_opengl
, AW_window_message
, AW_window_simple_menu
, AWT_graphic_exports
, AWT_graphic_tree
, AWT_scaled_font_limits
, BaseFrequencies
, BI_ecoli_ref
, BI_helix
, chartable::SepBaseFreq
, Column
, ED4_cursor
, ED4_reference_terminals
, FINAL_TYPE< SEQTYPE >
, FormattedFile
, GEN_map_window
, ItemShader
, NodeTextBuilder
, NT_TreeShader
, PH_filter
, probe_input_data
, pt_global
, SEC_root
, SpecSet
- init_alignment()
: ED4_root
- init_all_fonts()
: AW_gc_manager
- init_awars()
: FINAL_TYPE< SEQTYPE >
, RegFieldSelection
, ShaderPlugin
- init_click()
: FINAL_TYPE< SEQTYPE >
- init_color_ranges()
: AW_gc_manager
- init_device()
: AWT_canvas
- init_devices()
: AWT_graphic
, AWT_graphic_tree
, FINAL_TYPE< SEQTYPE >
, GEN_graphic
, RNA3D_Graphics
, SAI_graphic
- init_font()
: FINAL_TYPE< SEQTYPE >
- init_from_array()
: AW_selection_list
- init_life_counter()
: probe_combi_statistic
- init_object_specs()
: ED4_objspec
, ED4_objspec_registry
- init_results()
: ProbeMatchEventParam
- init_roulette_wheel()
: Generation
- init_specific_awars()
: ItemFieldShader
- init_static()
: POS_TREE1
, POS_TREE2
- init_stats()
: probe_combi_statistic
- init_toggler()
: SEC_db_interface
- init_tree()
: ARB_countedTree
, FINAL_TYPE< SEQTYPE >
- init_valuation()
: Generation
, ProbeValuation
- initFalseIDs()
: PS_Candidate
- initFromData()
: BI_helix
- initial_insert()
: AP_tree
, FINAL_TYPE< SEQTYPE >
- initial_progress()
: initial_progress
- initial_selfRef_progress()
: initial_selfRef_progress
- initial_update()
: ArbProgress::nestable
- initialise()
: ArbProbeMatchWeighting
, FINAL_TYPE< SEQTYPE >
- initialize()
: AP_tree_edge
, BasePosition
, GEN_map_manager
, GroupUIdata
, XString
- initialize_display()
: PH_display
- initialized()
: AutoMatchSettings
, GEN_map_manager
- InitMainFont()
: FINAL_TYPE< SEQTYPE >
- innermost_edge()
: EdgeFinder
- InputFileError()
: InputFileError
- InputFormat()
: InputFormat
- insert()
: ali_aligner_dellist
, ali_aligner_result
, ali_prealigner_approximation
, ali_prealigner_mask
, ALI_SUB_SOLUTION
, AP_tree
, AW_selection
, AW_selection_list
, ED4_SearchPosition
, FINAL_TYPE< SEQTYPE >
, GBL_streams
, Generation
, GenerationDuplicates
, GroupCluster
, List< Type >
, TrackedFiles
- insert_after()
: ALI_TLIST< T >
- insert_after_current()
: List< Type >
- insert_as_first()
: List< Type >
- insert_as_last()
: List< Type >
- insert_at_pos()
: List< Type >
- insert_at_pos_simple()
: List< Type >
- insert_before_current()
: List< Type >
- insert_bevor()
: ALI_TLIST< T >
- insert_data()
: GBENTRY
- insert_default()
: AW_selection
, AW_selection_list
- insert_default_option()
: AW_window
- insert_default_toggle()
: AW_window
- insert_folding_line()
: ED4_foldable
- insert_help_topic()
: AW_window
- insert_in_result_list()
: ProbeValuation
- insert_left()
: ali_aligner_last_cell
- insert_marker()
: ALI_MAP
- insert_member()
: ED4_container
- insert_menu_topic()
: AW_window
- insert_option()
: AW_window
- insert_plain()
: AW_selection
- insert_sorted_by_address_of_object()
: List< Type >
- insert_sub_menu()
: AW_window
- insert_toggle()
: AW_window
- insert_tree_weighted()
: ConsensusTree
- insert_unified_pattern()
: SearchTreeNode
- insert_up()
: ali_aligner_last_cell
- insert_window()
: ED4_window
- insertAs()
: ED4_folding_line
- insertations()
: ALI_MAP
- insertBefore()
: FieldTransfer::RuleSet
- InsertData()
: InsertData
- insertion()
: FastAlignReport
- insertionOrder_cmp()
: PART
- insertMapping()
: FINAL_TYPE< SEQTYPE >
- InsertPerfMeter()
: InsertPerfMeter
- insertSortedBy_matches()
: FamilyList
- insertSortedBy_rel_matches()
: FamilyList
- inside_auto_refresh()
: AWT_canvas
, AWT_graphic_exports
- inside_consensus_manager()
: ED4_base
- inside_group()
: probe_input_data
- inside_SAI_manager()
: ED4_base
- inside_species_seq_manager()
: ED4_base
- inside_update()
: AWT_graphic_exports
- insideLimits()
: RatioLimits
- inspect_CD1()
: Callback_FVF< RT, F1, F2 >
, Callback_FVV< RT, FIXED >
, Callback_VV< RT >
- inspect_CD2()
: Callback_FVF< RT, F1, F2 >
, Callback_FVV< RT, FIXED >
, Callback_VV< RT >
- install()
: AW_timer_cb_struct
- install_group_changed_callback()
: AWT_graphic_tree
- install_tree_changed_callback()
: AWT_graphic_tree
- instance()
: SpeciesFlags
, TREE_canvas_registry
- instant_refresh()
: AWT_canvas
- instant_resize()
: AWT_canvas
- instant_zoom_reset()
: AWT_canvas
- Int()
: Int< I >
- interpret_subcommand()
: GBL_call_env
- Interpreter()
: Interpreter
- intersect_with()
: AW::Rectangle
- intree_distance_to()
: TreeNode
- inUse()
: Output
- invalidate()
: ED4_base_position
, SEC_oriented
- invalidate_base_count()
: SEC_region
- invalidate_base_positions()
: SEC_root
- invalidate_species_counters()
: ED4_multi_species_manager
- invalidate_sub_angles()
: FINAL_TYPE< SEQTYPE >
, SEC_oriented
- inverse()
: ARB_edge
, DB_scalable
, RangeList
- inverse_without_inserts()
: ALI_MAP
- invert()
: PART
, PS_BitMap
, PS_BitSet
- invert_selection_of_all_species()
: ED4_multi_species_manager
- invertInSuperset()
: PART
- invisible()
: AW_device
- invisible_impl()
: AW_trackPositions_device
, AW_trackSpecies_device
- is()
: arb_test::group_match
- is3end()
: FINAL_TYPE< SEQTYPE >
- is_a_string()
: GBDATA
- is_above_clip()
: AW_clipable
- is_abstract_group_manager()
: ED4_base
- is_active_plugin()
: ItemShader
- is_allowed()
: TransTables
- is_ancestor_of()
: TreeNode
- is_area_manager()
: ED4_base
- is_auto_unfolded()
: AP_tree_folding
- is_begin()
: ALI_NORM_SEQUENCE
- is_below_clip()
: AW_clipable
- is_between()
: AW::Position
- is_block()
: Token
- is_bound_to_species()
: AP_sequence
- is_box()
: AW_clicked_element
- is_bracket_terminal()
: ED4_base
- is_branch()
: ClickedTarget
- is_cached()
: cache::CacheHandle< SMARTPTR >
- is_chain()
: POS_TREE1
, POS_TREE2
- is_child_of()
: ED4_base
- is_clade()
: TreeNode
- is_clear()
: MemBlockManager
, Memory
- is_client()
: GB_MAIN_TYPE
- is_color_group()
: gc_desc
- is_columnStat_terminal()
: ED4_base
- is_completely_visible()
: ED4_cursor
- is_consensus_manager()
: ED4_base
- is_consensus_sequence_terminal()
: ED4_base
- is_consensus_terminal()
: ED4_base
- is_consistent()
: ALI_TLIST< T >
- is_container()
: GBDATA
- is_correct_owner()
: ArbProgress::nestable
- is_dead()
: probe_combi_statistic
- is_defined()
: FINAL_TYPE< SEQTYPE >
, GBL_command_definition
, NoTuple
, ValueTuple
- is_detached()
: InfoWindow
- is_device_manager()
: ED4_base
- is_edge_from_leaf()
: ARB_edge
- is_edge_to_leaf()
: ARB_edge
- is_empty()
: ALI_TLIST< T >
, AW::FillStyle
, LinePart
, LooseBases
, PosRange
, Seq
- is_enabled()
: AW_helix
- is_endings_segment()
: FINAL_TYPE< SEQTYPE >
- is_entry()
: GBDATA
- is_equal()
: AbsLoc
, ALI_MAP
, AW_cb
, DataLoc
- is_equal_to()
: TypedDatabaseCallback
- is_expose_callback()
: AW_area_management
, AW_window
- is_flag_header_terminal()
: ED4_base
- is_flag_terminal()
: ED4_base
- is_focus_callback()
: AW_window
- is_folded()
: FoundGroup
- is_folded_group()
: AP_tree
- is_gene_result()
: ProbeMatchParser
- is_group_manager()
: ED4_base
- is_hidden()
: ED4_base
, ED4_manager
, ED4_terminal
, FINAL_TYPE< SEQTYPE >
- is_hidden_inside_group()
: ED4_cursor
- is_highlighted()
: FINAL_TYPE< SEQTYPE >
- is_ignored()
: BaseFrequencies
- is_imageref()
: Label
- is_in_folded_group()
: ED4_base
- is_in_helix()
: ALI_PROFILE
- is_indexable()
: GBDATA
- is_inferable()
: DupCriteria
- is_inner_edge()
: ARB_edge
- is_inner_node_with_remark()
: TreeNode
- is_inserted()
: ALI_MAP
- is_inside()
: TreeNode
- is_inside_folded_group()
: AP_tree
- is_internal_last()
: ALI_PROFILE
- is_invalid()
: AP_filter
- is_itemlist_member()
: FINAL_TYPE< SEQTYPE >
- is_keeled_group()
: TreeNode
- is_known()
: TreeRelativePosition
- is_konsistent()
: ALI_MAP
, ALI_SUB_SOLUTION
- is_leaf()
: POS_TREE1
, POS_TREE2
, TreeNode
- is_leaf_edge()
: AP_tree_edge
, PART
- is_leaf_set()
: SpecSet
- is_leftof_clip()
: AW_clipable
- is_leftson()
: TreeNode
- is_less_than()
: BoundTreeAwarCallback
- is_limited()
: PosRange
- is_line()
: AW_clicked_element
, ClickedTarget
- is_line_terminal()
: ED4_base
- is_linked()
: ED4_scrolled_rectangle
- is_linked_item()
: awt_mask_item
- is_linked_with()
: TopologyShader
- is_local_mask()
: awt_input_mask_global
, FINAL_TYPE< SEQTYPE >
- is_located()
: Group
- is_logically_zoomed()
: AWT_graphic_tree
- is_lower_son()
: ARB_seqtree
- is_maininfo()
: InfoWindow
- is_manager()
: ED4_base
, ED4_objspec
- is_mapped()
: AW_awar
- is_marked_for_removal()
: TypedDatabaseCallback
- is_marker()
: ClickedTarget
- is_monospaced()
: AW_font_limits
- is_multi_match()
: PartialSequence
- is_multi_name_manager()
: ED4_base
- is_multi_sequence_manager()
: ED4_base
- is_multi_species_manager()
: ED4_base
- is_name_manager()
: ED4_base
- is_node()
: POS_TREE1
, POS_TREE2
- is_normal_group()
: TreeNode
- is_normalized()
: AW::Vector
- is_orf_terminal()
: ED4_base
- is_outside_clip()
: AW_clipable
- is_outside_helix()
: ALI_PROFILE
- is_pairpos()
: BI_helix
, SEC_root
- is_part()
: PosRange
- is_part_of()
: TextRef
- is_partly_visible()
: ED4_cursor
- is_polygon()
: AW_clicked_element
- is_pure_text_terminal()
: ED4_base
- is_queried()
: QUERY::DbQuery
, QUERY::query_spec
- is_real_son_of()
: PART
- is_replaceable()
: BoundActionTracker
, NullTracker
, RequiresActionTracker
, UserActionTracker
- is_reset()
: ED4_foldable
- is_resize_callback()
: AW_area_management
, AW_window
- is_rightof_clip()
: AW_clipable
- is_rightson()
: TreeNode
- is_root_edge()
: AP_tree_edge
- is_root_group_manager()
: ED4_base
- is_root_loop()
: FINAL_TYPE< SEQTYPE >
- is_root_node()
: TreeNode
- is_ruler()
: ClickedTarget
- is_SAI_manager()
: ED4_base
- is_SAI_terminal()
: ED4_base
- is_saved()
: POS_TREE1
- is_sentinel()
: GBL_command_definition
- is_sequence_info_terminal()
: ED4_base
- is_sequence_manager()
: ED4_base
- is_sequence_terminal()
: ED4_base
- is_server()
: GB_MAIN_TYPE
- is_set()
: ED4_reference
, StrictlyTypedCallback< RT, P1, P2, P3 >
- is_shaded()
: AW::FillStyle
- is_shown()
: AW_window
, AWT_canvas
, ED4_remap
- is_single_value()
: LimitTracker< T >
- is_some_brother()
: FINAL_TYPE< SEQTYPE >
- is_son_of()
: TreeNode
- is_son_of_root()
: TreeNode
- is_spacer_terminal()
: ED4_base
- is_species_manager()
: ED4_base
- is_species_name_terminal()
: ED4_base
- is_species_seq_manager()
: ED4_base
- is_species_seq_terminal()
: ED4_base
- is_species_updated()
: AP_tree_root
- is_standardized()
: PART
- is_submatch()
: gb_hierarchy_location
- is_subset_of()
: PART
, TransTables
- is_terminal()
: ED4_base
, ED4_objspec
- is_text()
: AW_clicked_element
, ClickedTarget
- is_text_terminal()
: ED4_base
- is_tracking()
: AW_root
, UserActionTracker
- is_tree_updated()
: AP_tree_root
- is_undefined()
: ALI_MAP
- is_unlimited()
: PosRange
- is_unweighted()
: AP_weights
- is_up()
: Flag
- is_up_to_date()
: MostLikelySeq
- is_upper_son()
: ARB_seqtree
- is_used()
: InfoWindow
- is_valid()
: AW_awar
, gb_hierarchy_location
, Group
, PART
- is_valid_between()
: AliData
- is_valid_part()
: AliData
- is_valid_pos()
: AliData
, CentigradePos
- is_viewport()
: awt_mask_item
- is_weighted()
: ArbProgress::weightable
- is_whole()
: PosRange
- isAbove()
: isAbove< T >
- isAssigned()
: UsedColor
- isBelow()
: isBelow< T >
- isBetterThan()
: PartitionSpec
- IsCallback()
: IsCallback
- isCompressed()
: KeyInfo
- isConnectedTo()
: AP_tree_edge
- isGap()
: BaseFrequencies
, export_sequence_data
- isInRange()
: ComplementLocation
, JoinedLocation
, Location
, SimpleLocation
- IslandHopping()
: FINAL_TYPE< SEQTYPE >
- IslandHoppingParameter()
: FINAL_TYPE< SEQTYPE >
- isLeaf()
: Node
- isMarked()
: MarkedPrefixes
- isMatched()
: FINAL_TYPE< SEQTYPE >
- isNull()
: SizedCstr
, SmartPtr< T, C >
- isolate_list_elem()
: list_elem< Type >
- isOutputPipe()
: zinfo
- isPerfectMatch()
: GroupPenalty
- isPrimer()
: Node
- isReadonly()
: FINAL_TYPE< SEQTYPE >
, PS_FileBuffer
- isRootsideFixpoint()
: FINAL_TYPE< SEQTYPE >
- isSet()
: CharRangeTable
, SizedCstr
, SmartPtr< T, C >
- IsSpecificCallback()
: IsSpecificCallback
- IsSpecificHierarchyCallback()
: IsSpecificHierarchyCallback
- isStartCodon()
: AWT_translator
- isStartOrStopCodon()
: AWT_translator
- isStdColor()
: UsedColor
- isStopCodon()
: AWT_translator
- isValid()
: RatioLimits
- isValidPrimer()
: Node
- isVoid()
: Parameter
, Type
- item()
: awt_linked_to_item
- Item()
: Item
- ItemClonedByRuleSet()
: FieldTransfer::ItemClonedByRuleSet
- Itemfield_Selection()
: Itemfield_Selection
- ItemFieldShader()
: ItemFieldShader
- ItemQueryKey()
: FINAL_TYPE< SEQTYPE >
- ItemShader()
: ItemShader
- ItemShader_impl()
: FINAL_TYPE< SEQTYPE >
- iterate()
: ExplicitQueryKey
, FINAL_TYPE< SEQTYPE >
, ParentGroupNameQueryKey
, QueryKey
- iterateWith()
: SearchFIFO
- iteration_count()
: ARB_edge