- c -
- c_decl()
: Type
- c_str()
: Ostring
- c_typed_param()
: Parameter
- Cache()
: cache::Cache< SMARTPTR >
- cache_is_flushed()
: MarkerDisplay
- cache_Sonde()
: ST_Container
- CacheHandle()
: cache::CacheHandle< SMARTPTR >
- calc_best_area()
: SlaveCanvas_internal
- calc_best_scroll_delta()
: SlaveCanvas_internal
- calc_bottomRight_folding_dimensions()
: ED4_scrolled_rectangle
- calc_bounding_box()
: ED4_base
, ED4_manager
, ED4_terminal
- calc_branchlengths()
: AP_tree_edge
- calc_centigrade_pos()
: MatchingOligo
- calc_clade_level()
: TreeNode
- calc_expected_children()
: probe_combi_statistic
- calc_fitness()
: probe_combi_statistic
- calc_group_depth()
: ED4_base
- calc_helix_count()
: Structure3D
- calc_index_system3()
: probe_combi_statistic
- calc_inner_GC()
: AP_TreeShader
- calc_interval_displayed_in_rectangle()
: ED4_abstract_sequence_terminal
- calc_leaf_GC()
: AP_TreeShader
- calc_max_used_words()
: Clusterer
- calc_nesting_level()
: GroupSearch
- calc_out()
: MostLikelySeq
- calc_rel_coords()
: ED4_base
- calc_rel_match()
: HitCounter
- calc_rel_matches()
: FamilyStat
- calc_relpos()
: probe_input_data
- calc_shaded_inner_GC()
: AP_DefaultTreeShader
, AP_TreeShader
, NT_TreeShader
- calc_shaded_leaf_GC()
: AP_DefaultTreeShader
, AP_TreeShader
, NT_TreeShader
- calc_st_ml()
: ST_ML
- calc_update_interval()
: ED4_abstract_sequence_terminal
- calc_value()
: FieldReader
, MultiFieldReader
- calc_world_coords()
: ED4_base
- calcEdgeDistance()
: RootSynchronizer
- calcFitness()
: Generation
- calcOverallCounter()
: BaseCounter
- calcTaxDiffLevel()
: SpeciesInTwoTrees
- calcTreeDistance()
: RootSynchronizer
- calcTreeInfo()
: ARB_seqtree
- calculate()
: ColumnStat
, DI_MATRIX
, QuadraticThreshold
- calculate_ancestor()
: MostLikelySeq
- calculate_column_homology()
: PH_filter
- calculate_header_dimensions()
: SpeciesFlags
- calculate_helix_coordinates()
: FINAL_TYPE< SEQTYPE >
- calculate_helix_size()
: FINAL_TYPE< SEQTYPE >
- calculate_loop_coordinates()
: FINAL_TYPE< SEQTYPE >
- calculate_loop_size()
: FINAL_TYPE< SEQTYPE >
- calculate_outgroup_matches()
: OutgroupMatcher
- calculate_pro()
: DI_MATRIX
- calculate_scrollbars()
: AW_window
- calculate_segment_coordinates()
: FINAL_TYPE< SEQTYPE >
- calculate_segment_size()
: FINAL_TYPE< SEQTYPE >
- calcUnknownMembersPenalty()
: GroupMatchScorer
- call()
: AW_root_cblist
, AW_timer_cb_struct
, BoundTreeAwarCallback
, Command
, ED4_cb_list< BASE, BASECB >
, FINAL_TYPE< SEQTYPE >
, gb_callback
, gb_callback_list
, NoSuchCommand
, SEC_dbcb
, Store_species
- call_and_forget()
: gb_pending_callbacks
- call_arguments()
: Prototype
- call_pending_callbacks()
: GB_MAIN_TYPE
- callAfter()
: AW_timer_cb_struct
- callAll()
: TrackedFile
- callback()
: AW_window
, PS_Callback
- Callback_FFV()
: Callback_FFV< RT, F1, F2 >
- Callback_FVF()
: Callback_FVF< RT, F1, F2 >
- Callback_FVV()
: Callback_FVV< RT, FIXED >
- callback_if_changed()
: TrackedFile
- Callback_VV()
: Callback_VV< RT >
- CallbackData()
: CallbackData< P1, P2 >
- callee()
: Callback_FVF< RT, F1, F2 >
, Callback_FVV< RT, FIXED >
, Callback_VV< RT >
- calling_child_progress()
: FINAL_TYPE< SEQTYPE >
- callOrDelayIfDisabled()
: AW_timer_cb_struct
- canDecompress()
: Dict
- Candidate()
: Candidate
- canDisplay()
: SEC_db_interface
, SEC_root
- cantMoveNextTo()
: AP_tree
- canvas()
: SEC_db_interface
- CanvasRef()
: CanvasRef
- cardinality()
: ALI_TLIST< T >
- case_op()
: case_op
- cast_to_AW_CL()
: AW_CL_castableType< T >
- cat()
: GBS_strstruct
- cat_dQuoted()
: GBS_strstruct
- cat_sQuoted()
: GBS_strstruct
- cat_wrapped()
: GBS_strstruct
- catched()
: Convaln_exception
- catPadded()
: GBS_strstruct
- cd1()
: AW_clicked_element
- cd2()
: AW_clicked_element
- center_xpos()
: SpeciesFlag
- centerx()
: MarkerXPos
- centigrade_pos_out_of_reach()
: MatchingOligo
- centroid()
: AW::LineVector
- ChainEntryBuffer()
: ChainEntryBuffer
- ChainIteratorStage1()
: ChainIteratorStage1
- ChainIteratorStage2()
: ChainIteratorStage2
- change_folding()
: FoundGroup
- change_from_widget()
: VarUpdateInfo
- change_listed_groups_folding()
: GroupUIdata
- change_parsimony_start()
: QuadraticThreshold
- change_root()
: AP_tree_root
, TreeRoot
- change_table_length()
: BaseFrequencies
, chartable::SepBaseFreq
- changed_by_database()
: ED4_base
, ED4_manager
, ED4_terminal
- changed_range()
: BaseFrequencies
- changeSortOrder()
: ClustersData
- changeType()
: ED4_cursor
- char_to_enum()
: DNA_Table
- CharCounter()
: CharCounter
- CharPredicate()
: CharPredicate
- CharPtrArray()
: CharPtrArray
- CharRangeTable()
: CharRangeTable
- cheapest_sequence()
: ALI_PROFILE
- check()
: ALI_SEQUENCE
, ARB_type_traits::is_base_of< B, D >
, Splits
- check1()
: ARB_type_traits::is_same< T, U >
- check2()
: ARB_type_traits::is_same< T, U >
- check_all()
: ED4_base
- check_applicable_to()
: AliAutoFormatCommand
, AliCompositeCommand
, AliDeleteCommand
, AliEditCommand
, AliInsertCommand
, FINAL_TYPE< SEQTYPE >
- check_base_counters()
: Importer
- check_changes()
: TrackedFiles
- check_delete_allowed()
: AliData
- check_dimension_change()
: FINAL_TYPE< SEQTYPE >
, ItemShader
- check_duplicates()
: probe_combi_statistic
- check_for_DB_update()
: AWT_graphic
, AWT_graphic_tree
, AWT_nonDB_graphic
, FINAL_TYPE< SEQTYPE >
, GEN_graphic
- check_for_min()
: Sonde
- check_for_results()
: Generation
- check_hkey()
: FieldTransfer::WriteRule
- check_in_bases()
: ED4_manager
- check_lengths_equal()
: SaiCalcEnv
- check_out_bases()
: ED4_manager
- check_overflow()
: ST_base_vector
- check_properties()
: AW_root
- check_result()
: NamedCommand
- check_update()
: AP_tree_root
, FINAL_TYPE< SEQTYPE >
- check_valid()
: customCriterion
- check_valid_scrollbar_values()
: ED4_window
- check_validity()
: GroupMatchScorer
- CheckedConsistencies()
: CheckedConsistencies
- checkOverallCounter()
: BaseCounter
- checksum()
: AP_combinableSeq
, ChecksumCollector
, FINAL_TYPE< SEQTYPE >
- ChecksumCollector()
: ChecksumCollector
- child_progress()
: FINAL_TYPE< SEQTYPE >
- child_sets_text()
: ArbProgress::nestable
- child_terminated()
: ArbProgress::nestable
- child_updates_gauge()
: ArbProgress::counter
, FINAL_TYPE< SEQTYPE >
, no_counter
, null_counter
- childByBase()
: Node
- ChildLookupTable()
: ChildLookupTable
- circle()
: AW_device
- cleanup()
: GroupUIdata
, probe_struct_global
, ST_ML
- clear()
: AISC_Object
, ali_aligner_result
, ali_prealigner_approximation
, ali_prealigner_mask
, ALI_TSTACK< T >
, AP_tree_members
, ArbProbeCollection
, AW_device
, AW_root_cblist
, AW_screen_area
, AW_selection_list
, AW_world
, AWT_graphic_tree_group_state
, CharCounter
, CharPtrArray
, ClustersData
, CursorPos
, ED4_cb_list< BASE, BASECB >
, ED4_container
, ED4_coords
, ED4_reference
, ED4_reference_terminals
, FINAL_TYPE< SEQTYPE >
, GroupChanges
, GroupCluster
, LooseBases
, MemBlockManager
, Memory
, MostUsedPos
, PH_display_status
, PS_FileBuffer
, SEC_drawn_positions
, StrUniquifier
- clear_all()
: ST_ML
- clear_announced_positions()
: SEC_root
- clear_background()
: ED4_base
- clear_error()
: AliData
- clear_failure()
: Realigner
- clear_fathers()
: POS_TREE1
- clear_last_drawed_cursor_position()
: SEC_root
- clear_notifications()
: GroupSearchCommon
- clear_option_menu()
: AW_window
- clear_part()
: AW_device
, FINAL_TYPE< SEQTYPE >
- clear_refresh()
: ED4_manager
- clear_refresh_request()
: AWT_graphic_exports
- clear_resize_request()
: AWT_graphic_exports
- clear_result_list()
: GroupUIdata
- clear_SAI_filters()
: FilteredExport
- clear_save_request()
: AWT_graphic_exports
- clear_structure_update_request()
: AWT_graphic_exports
- clear_tags()
: FINAL_TYPE< SEQTYPE >
- clear_whole_background()
: FINAL_TYPE< SEQTYPE >
- clear_window()
: PH_display
- clear_zoom_reset_request()
: AWT_graphic_exports
- clearMarks()
: MarkedPrefixes
- CLI()
: CLI
- ClickedElement()
: ClickedElement
- ClickedTarget()
: ClickedTarget
- ClientActionTracker()
: ClientActionTracker
- clip()
: AW_clipable
- clip_screen_range()
: ED4_remap
- clipped_sequence_to_screen_PLAIN()
: ED4_remap
- clone()
: ArbProgress::counter
, AW_clicked_box
, AW_clicked_element
, AW_clicked_line
, AW_clicked_text
, FINAL_TYPE< SEQTYPE >
, no_counter
, NoTuple
, null_counter
, PART
, SQ_GroupData
, SQ_GroupData_RNA
, ValueTuple
- close()
: ALI_ARBDB
, BasicStatus
, BufferedPipeReader
, FINAL_TYPE< SEQTYPE >
, GB_transaction
, Output
, XML_Comment
, XML_Node
, XML_Text
- close_and_unlink()
: Output
- close_db()
: SelectedDatabase
- close_global_shell()
: GB_test_shell_closed
- close_sub_menu()
: AW_window
- clr_property()
: ED4_base
- Cluster()
: Cluster
- Clusterer()
: Clusterer
- ClustersData()
: ClustersData
- ClusterTree()
: FINAL_TYPE< SEQTYPE >
- ClusterTreeRoot()
: FINAL_TYPE< SEQTYPE >
- clusterWithID()
: ClustersData
- Cma()
: FINAL_TYPE< SEQTYPE >
- cmd()
: AWT_graphic_event
- cmp_abs()
: FamilyStat
, HitCounter
- cmp_combined()
: AP_combinableSeq
, FINAL_TYPE< SEQTYPE >
- cmp_data()
: AliData
, AliDataSlice
, FINAL_TYPE< SEQTYPE >
, LazyAliData
, SpecificAliData< T >
, SpecificGap< T >
- cmp_rel()
: FamilyStat
, HitCounter
- cmp_whole_data()
: AliData
- cmpPartWith()
: AliData
- Code()
: Code
- CodeNr()
: AWT_translator
- codon2aa()
: AWT_translator
- Codon_Group()
: Codon_Group
- collect()
: ChecksumCollector
- collect_byte()
: ChecksumCollector
- collect_hits_for()
: MatchRequest
- collect_mem()
: ChecksumCollector
- collect_subset_cb()
: AW_subset_selection
- color_groups_initialized()
: AW_gc_manager
- colorize()
: AP_tree
- ColorMap()
: ColorMap
- ColorRGBf()
: ColorRGBf
- Column()
: Column
- column()
: column
- column_stat()
: ED4_reference_terminals
- column_stat_info()
: ED4_reference_terminals
- ColumnQualityInfo()
: ColumnQualityInfo
- ColumnStat()
: ColumnStat
- ColumnWidths()
: ColumnWidths
- CombinableSeq()
: CombinableSeq
- combine()
: DendroSubtreeLimits
- Combine2Dand3DstructureInfo()
: Structure3D
- combine_count()
: AP_combinableSeq
- combine_seq()
: AP_combinableSeq
, FINAL_TYPE< SEQTYPE >
- combinedEquals()
: AP_combinableSeq
- CombinedPosInfo()
: CombinedPosInfo
- combines_performed()
: PARSIMONY_testenv< SEQTYPE >
- CommandOutput()
: CommandOutput
- comment_writer()
: GcgWriter
- commentList()
: FINAL_TYPE< SEQTYPE >
- CommentSkippingFileBuffer()
: CommentSkippingFileBuffer
- commit_transaction()
: ALI_ARBDB
, GB_MAIN_TYPE
- CompactedSequence()
: CompactedSequence
- CompactedSubSequence()
: CompactedSubSequence
- compare()
: AW_cb
, CombinedPosInfo
, TextRef
, TreeRelativePosition
- compare_by_criteria()
: compare_by_criteria
- compile()
: ED4_remap
- compile_needed()
: ED4_remap
- Complement()
: Complement
, GEN_gene
- complement_position()
: ALI_PROFILE
- ComplementLocation()
: ComplementLocation
- completely_bound()
: MatchingOligo
- completely_clipped()
: AW_clipable
- completely_shows()
: ED4_window
- compoutcode()
: AW_clipable
- compPosition()
: CompactedSequence
, CompactedSubSequence
- compress()
: DI_MATRIX
- CompressionRoot()
: CompressionRoot
- CompressionTree()
: FINAL_TYPE< SEQTYPE >
- compute_mituples()
: FINAL_TYPE< SEQTYPE >
- compute_tree()
: AP_tree
, ARB_countedTree
, FINAL_TYPE< SEQTYPE >
, PARSIMONY_testenv< SEQTYPE >
, TreeNode
- ComputeBasePositions()
: Structure3D
- computeClusters()
: FINAL_TYPE< SEQTYPE >
- computeMutualInformation()
: FINAL_TYPE< SEQTYPE >
- computeMutualInformationP()
: FINAL_TYPE< SEQTYPE >
- concatenated()
: GBL_streams
- concrete_counter()
: FINAL_TYPE< SEQTYPE >
- config_string()
: AWT_config
, ConfigMapping
- ConfigDefinition()
: ConfigDefinition
- ConfigDeleter()
: ConfigDeleter
- ConfigMarkerDisplay()
: FINAL_TYPE< SEQTYPE >
- ConfigRenamer()
: ConfigRenamer
- configure_active_plugin()
: FINAL_TYPE< SEQTYPE >
- configure_active_plugin_cb()
: FINAL_TYPE< SEQTYPE >
- configure_colors_cb()
: FINAL_TYPE< SEQTYPE >
- connect()
: NameServerConnection
- ConsensusReference()
: ConsensusReference
- ConsensusTree()
: ConsensusTree
- ConstStrArray()
: ConstStrArray
- containing_species_manager()
: ED4_base
- contains()
: AW::Rectangle
, AW_cb
, AW_root_cblist
- Contains()
: CommandOutput
- contains()
: FINAL_TYPE< SEQTYPE >
, GroupCluster
, MemBlock
, Partition
, PosRange
, Range
- contains_changed()
: QueriedGroups
- contains_marked_species()
: ARB_seqtree
- contains_seq_position()
: SEC_region
- contains_unremoved_callback()
: CallbackList< CB >
- containsPos()
: ED4_SearchPosition
- Content()
: FINAL_TYPE< SEQTYPE >
- content()
: SmartPtr< T, C >
- Convaln_exception()
: Convaln_exception
- convert()
: ED4_reference
- convert_argument_for_C()
: Type
- convert_BackgroundGC()
: PaintData
- convert_result_for_PERL()
: Type
- ConvertGCtoRGB()
: FINAL_TYPE< SEQTYPE >
- ConvertibleData()
: ConvertibleData
- convertTreesToLists()
: PrimerDesign
- copy()
: AlignBuffer
, arb_test::copy< T >
, arb_test::copy< const char * >
, BufferPtr< T >
, FINAL_TYPE< SEQTYPE >
, PrefixIterator
, PS_BitMap
, PS_BitSet
, TextRef
- copy_corresponding_part()
: PosRange
- copy_multi_rem()
: FINAL_TYPE< SEQTYPE >
- copy_window_struct()
: ED4_root
- copyPartTo()
: AliData
- copyTo()
: AliData
, LinePart
, LineReader
, SEC_structure_toggler
- correctUnalignedPositions()
: AlignBuffer
- corresponding_columnStat_terminal()
: ED4_sequence_terminal
- corresponding_sequence_terminal()
: FINAL_TYPE< SEQTYPE >
- corresponding_species_name_terminal()
: ED4_abstract_sequence_terminal
, FINAL_TYPE< SEQTYPE >
- cos()
: AW::Angle
- costs()
: FINAL_TYPE< SEQTYPE >
- count()
: ClustersData
, ComplementLocation
, JoinedLocation
, Location
, LowDataCheck
, Seq
, SimpleLocation
- count_aligned_base()
: FastAlignReport
- count_clades()
: TreeNode
- count_distance()
: DistanceCounter
- count_elements()
: AP_STACK< ELEM >
- count_fulfilled()
: arb_test::expectation_group
- count_gaps()
: Seq
- count_leafs()
: AP_tree
- count_match()
: FamilyStat
- count_mutpsite()
: count_mutpsite
- count_registered()
: ED4_objspec_registry
- count_rules()
: SaiBoolchainOperator
- count_species()
: export_sequence_data
- count_species_in_tree()
: ST_ML
- count_unaligned_base()
: FastAlignReport
- count_unweighted()
: count_unweighted
- count_value()
: ValueCounter< T >
- count_versus()
: Mismatches
- count_visible_children()
: ED4_multi_species_manager
- count_weighted()
: count_weighted
, Mismatches
- count_weighted_bases()
: AP_combinableSeq
- countChars()
: CharCounter
- countChildren()
: PS_Node
- Counted()
: Counted< T, AP >
- counter()
: ArbProgress::counter
- counter_next()
: ARB_edge
- counter_previous()
: ARB_edge
- countProbes()
: PS_Node
- countSpeciesAndData()
: ImportTestData
- countTextNodes()
: FINAL_TYPE< SEQTYPE >
- create()
: ArbProgress::nestable
, DbScanner
, FormatReader
, SequenceHandler
- create_aliview()
: WeightedFilter
- create_autosize_button()
: AW_window
- create_awars()
: AP_userdef_matrix
, ed_key
- create_button()
: AW_window
- create_child_progress()
: ArbProgress::nestable
, FINAL_TYPE< SEQTYPE >
, initial_progress
, null_progress
- create_column_statistic()
: ST_ML
- create_common_gui()
: FormatTester
- create_consensus()
: ED4_manager
- create_default_bone()
: SEC_root
- create_devices()
: AW_area_management
, AW_window
- create_extended()
: GBDATA
- create_filter()
: WeightedFilter
- create_first_window()
: ED4_root
- create_folding_lines()
: ED4_scrolled_rectangle
- create_gap()
: AliData
, AliDataSlice
, FINAL_TYPE< SEQTYPE >
, LazyAliData
, SequenceAliData
, TypedAliData< T >
- create_gc()
: AW_common_Xm
- create_gc_buttons()
: AW_gc_manager
- create_gcs()
: AW_xfig
- create_GEN_position()
: Location
- create_GEN_position_from_fields()
: LocationEditor
- create_gui_elements()
: File_selection
- create_hierarchy()
: ED4_root
- create_input_field()
: AW_window
- create_input_field_with_scaler()
: AW_window
- create_input_fields()
: AP_userdef_matrix
- create_inverse_toggle()
: AW_window
- create_invisible()
: AW_window
- create_list()
: SelectionListSpec
- create_menu()
: AW_window
- create_mode()
: AW_window
- create_next_generation()
: Generation
- create_option_menu()
: AW_window
- create_result_window()
: MP_Window
- create_root()
: PartitionSize
- create_sai_selection_list()
: ColumnStat
- create_selection_list()
: AW_window
- create_suppressor()
: ArbProgress::nestable
- create_text_field()
: AW_window
- create_text_toggle()
: AW_window
- create_toggle()
: AW_window
- create_toggle_field()
: AW_window
- create_tprobes()
: ProbeCandidates
- create_tree_PART()
: SpeciesSpace
- create_tree_root()
: AWT_graphic_tree
- create_user_geometry_awars()
: AW_window
- create_weights()
: WeightedFilter
- create_window()
: RegFieldSelection
- create_window_variables()
: AW_window
- createButton()
: SelectionListSpec
- createEditFields()
: LocationEditor
- createFrom()
: PT_compressed
- createGeneName()
: Feature
- createOrganism()
: DBwriter
- creation_date()
: GBDATA
- crossover_Probes()
: probe_combi_statistic
- current()
: ALI_TLIST< T >
, awt_item_type_selector
, EXP_item_type_species_selector
, FINAL_TYPE< SEQTYPE >
, GB_securityLevel
, GEN_item_type_species_selector
- CursorPos()
: CursorPos
- cursorpos()
: cursorpos
- custom_dealloc_ptr()
: custom_dealloc_ptr< T, DEALLOC >
- customCriterion()
: customCriterion
- customizable()
: ItemFieldShader
, ShaderPlugin
, TopologyShader
- customize()
: ItemFieldShader
, ShaderPlugin
, TopologyShader
- cut()
: GBS_strstruct
- cut_tail()
: GBS_strstruct