- p -
- Package()
: Package
- padding()
: ArbMatchResult
- paint()
: FINAL_TYPE< SEQTYPE >
, GEN_root
, RNA3D_Graphics
, SAI_graphic
, SEC_bond_def
, SEC_root
- paint_constraints()
: FINAL_TYPE< SEQTYPE >
- paint_strands()
: FINAL_TYPE< SEQTYPE >
- paintAnnotation()
: SEC_root
- paintBackgroundColor()
: SEC_root
- PaintData()
: PaintData
- PaintedNode()
: PaintedNode
- paintPosAnnotation()
: SEC_root
- paintSearchPatternStrings()
: SEC_root
- Pair()
: Pair
- pair_strength()
: BI_pairdef
- panic_save()
: GB_MAIN_TYPE
- PaperFormat()
: PaperFormat
- param_count()
: GBL_command_arguments
- Parameter()
: Parameter
- parameters()
: parameters
- parent()
: SEC_base_part
, SEC_oriented
- parent_block()
: TokenList
- parent_block_token()
: Token
- parent_list()
: Token
- ParentGroupNameQueryKey()
: ParentGroupNameQueryKey
- PARS_commands()
: PARS_commands
- parse()
: AttributeParser
, NtreeCommandLine
- parse_bootstrap()
: TreeNode
- parse_decl()
: gc_desc
- parse_entry()
: Parser
- parse_program()
: Parser
- parse_section()
: EmblParser
, GenbankParser
, MackeParser
, Parser
- ParsedProbeMatch()
: ParsedProbeMatch
- parseError()
: AWT_config
- parseFeature()
: Importer
- parseFeatureTable()
: Importer
- parseFrom()
: ConfigMapping
- Parser()
: Parser
- parseTokenListBlock()
: Parser
- parsimony_rec()
: FINAL_TYPE< SEQTYPE >
- PARSIMONY_testenv()
: PARSIMONY_testenv< SEQTYPE >
- PART()
: PART
- partBefore()
: TextRef
- partBehind()
: TextRef
- partial_match()
: AP_combinableSeq
, FINAL_TYPE< SEQTYPE >
- PartialSequence()
: PartialSequence
- Partition()
: Partition
- partition()
: PartitionSpec
- PartitionSize()
: PartitionSize
- PartitionSpec()
: PartitionSpec
- partly_shows()
: ED4_window
- PartQueue()
: PartQueue
- PartRegistry()
: PartRegistry
- pass_probability()
: Partition
- passed()
: ARB_timeout
- paste_at()
: GBS_strstruct
- Paup()
: Paup
- pc()
: Command
- PD_formatter()
: PD_formatter
- peek()
: PS_FileBuffer
- peek_format()
: ArbImporter
- peek_key_event()
: AW_root
- peek_part()
: DeconstructedTree
, PartRegistry
- peekImportDB()
: ArbImporter
- pending()
: gb_pending_callbacks
- percent()
: ColumnWidths
- perform()
: Dragged
- perform_action()
: awt_mask_action
- perform_all()
: SimpleTester
- perform_autoscroll()
: SEC_root
- perform_check()
: CheckedConsistencies
- perform_item_checks()
: CheckedConsistencies
- perform_marking()
: DepthMarker
- perform_search()
: GroupSearch
- PerfTimer()
: PerfTimer
- perl_decl()
: Type
- perl_typed_param()
: Parameter
- permitPrecisionLoss()
: FieldTransfer::Rule
- PersistantFlag()
: PersistantFlag
- persistence()
: NameServerConnection
- PersistentNameServerConnection()
: PersistentNameServerConnection
- PH_display()
: PH_display
- PH_display_status()
: PH_display_status
- PH_filter()
: PH_filter
- PH_NEIGHBOUR_DIST()
: PH_NEIGHBOUR_DIST
- PH_NEIGHBOURJOINING()
: PH_NEIGHBOURJOINING
- PH_root()
: PH_root
- PH_used_windows()
: PH_used_windows
- phase_changed_cb()
: FINAL_TYPE< SEQTYPE >
- Phaser()
: Phaser
- PHDATA()
: PHDATA
- pixel2pos()
: ED4_root
- plain_pointer()
: RefPtr< T >
- PlanarTuple()
: FINAL_TYPE< SEQTYPE >
- PlotParam()
: PlotParam
- PlugIn()
: PlugIn
- plugin_awar()
: ShaderPlugin
- PO_Less()
: PO_Less
- point()
: output
- pointer_ref()
: RefPtr< T >
- pointsToOutside()
: FINAL_TYPE< SEQTYPE >
- PointsToQuads()
: Structure3D
- pointsToRoot()
: FINAL_TYPE< SEQTYPE >
- polygon()
: AW_device
- pop()
: ALI_TSTACK< T >
, AP_STACK< ELEM >
, PARSIMONY_testenv< SEQTYPE >
, PrintMaybe
- pop_clip_scale()
: AW_device
- pop_transaction()
: AWT_canvas
, GB_MAIN_TYPE
- pop_will_produce_valid_tree()
: PARSIMONY_testenv< SEQTYPE >
- popdown()
: RegFieldSelection
- popup()
: SelectionListSpec
- popup_config()
: NT_TreeShader
- popup_config_window()
: FINAL_TYPE< SEQTYPE >
, ItemShader
- popup_edit_window()
: AWT_configuration
- popup_window()
: RegFieldSelection
- pos()
: MarkerPosition
, RegMatch
- posBehindMatch()
: RegMatch
- PosGene()
: PosGene
- position()
: ALI_MAP
- Position()
: AW::Position
- position()
: AWT_graphic_event
- position_cursor()
: SEC_root
- PositionPair()
: PositionPair
- positions()
: HelixAlignmentQuality
- PositionsToCoordinatesDispList()
: Structure3D
- PosRange()
: PosRange
- possible_as_xsub()
: Prototype
- possible_in_xsub()
: Type
- precisionLossPermitted()
: FieldTransfer::Rule
- predecessor()
: FINAL_TYPE< SEQTYPE >
- predecide()
: MarkedPrefixes
- predelete()
: TreeRoot
- predicate()
: arb_test::predicate< FUNC >
- predicate_description()
: arb_test::predicate_description
- predicate_expectation()
: arb_test::FINAL_TYPE< T >
- predicate_matcher()
: arb_test::predicate_matcher< T, FUNC >
- prefix()
: PrefixIterator
- PrefixIterator()
: PrefixIterator
- PrefixProbabilities()
: PrefixProbabilities
- preload_rel2abs()
: probe_input_data
- prepare_input_data()
: SaiBoolRule
- prepare_itemfield()
: SpeciesFlag
- PREPARE_MARK_NONFINAL_CLASS()
: AP_tree
, AP_tree_root
, ARB_seqtree_root
, AW_window_menu_modes
, AWT_graphic_tree
, BufferedFileReader
, ConstStrArray
, ED4_sequence_terminal
, FileWriter
, Reader
- prepare_paint()
: FINAL_TYPE< SEQTYPE >
- prepare_shutdown()
: ED4_base_position
, ED4_cursor
- prepend_elem()
: ED4_list< T >
- preserve()
: ARB_ERROR
- prev()
: ALI_TLIST< T >
- previous()
: ARB_edge
, GB_securityLevel
, GroupIterator
- PrimerDesign()
: PrimerDesign
- print()
: ali_aligner_cell
, ali_aligner_column
, ali_aligner_dellist
, ali_aligner_dellist_elem
, ali_aligner_last_cell
, ALI_MAP
, ALI_PATHMAP
, ali_prealigner_approx_element
, ali_prealigner_approximation
, ALI_PROFILE
, ALI_SUB_SOLUTION
, ALI_TLIST< T >
, ALI_TLIST_ELEM< T >
, AP_rates
, AW_xfig
, Bitvector
, ColumnStat
, DiffLines
, Error
, FINAL_TYPE< SEQTYPE >
, Generation
, InputFileError
, Item
, MostLikelySeq
, Node
, Pair
, probe_combi_statistic
, probe_tabs
, ProgramError
, PS_BitMap
, PS_BitSet
, PS_Candidate
, PS_Node
, Range
, SearchFIFO
, Smoother
, Sonde
, ST_base_vector
, ST_rate_matrix
, WrapMode
- print_cont()
: ali_aligner_dellist
- print_error()
: UnitTest_simple
- print_error_internal()
: Code
, Location
- print_from()
: DiffLines
- print_help()
: NtreeCommandLine
- print_info()
: PartitionSpec
- print_readable_string()
: arb_test::StaticCode
- print_string()
: FINAL_TYPE< SEQTYPE >
- print_warning_internal()
: Code
, Location
- print_xsubs()
: Package
, xsubGenerator
- printCountAndMem()
: PT_statistic
- printCountPercentAndMem()
: PT_statistic
- printf()
: arb_test::StaticCode
- printGNUplot()
: FINAL_TYPE< SEQTYPE >
, PS_BitMap
- PrintMaybe()
: PrintMaybe
- printOnlyMe()
: PS_Node
- printProbes()
: PS_Candidate
- PrintString()
: FINAL_TYPE< SEQTYPE >
- printUserColorDefinitions()
: ColorMap
- prior()
: PosRange
- probe()
: FINAL_TYPE< SEQTYPE >
- probe_combi_statistic()
: probe_combi_statistic
- probe_input_data()
: probe_input_data
- probe_tabs()
: probe_tabs
- ProbeCandidates()
: ProbeCandidates
- ProbeCollDisplay()
: ProbeCollDisplay
- ProbeCommonSettings()
: ProbeCommonSettings
- ProbeIterator()
: ProbeIterator
- probeList()
: ArbProbeCollection
- ProbeMatch_impl()
: ProbeMatch_impl
- ProbeMatchEventParam()
: ProbeMatchEventParam
- ProbeMatchParser()
: ProbeMatchParser
- ProbeMatchSettings()
: ProbeMatchSettings
- ProbeOccurrence()
: ProbeOccurrence
- ProbeValuation()
: ProbeValuation
- process_events()
: AW_root
- process_pending_events()
: AW_root
- ProgramError()
: ProgramError
- PromptData()
: PromptData
- protein_at()
: FailedAt
- Prototype()
: Prototype
- PS_BitMap()
: PS_BitMap
- PS_BitMap_Counted()
: FINAL_TYPE< SEQTYPE >
- PS_BitMap_Fast()
: FINAL_TYPE< SEQTYPE >
- PS_BitSet()
: PS_BitSet
- PS_BitSet_Fast()
: FINAL_TYPE< SEQTYPE >
- PS_Candidate()
: PS_Candidate
- PS_Database()
: FINAL_TYPE< SEQTYPE >
- PS_FileBuffer()
: PS_FileBuffer
- PS_Node()
: PS_Node
- PT_compressed()
: PT_compressed
- PT_dump_loc()
: PT_dump_loc
- PT_FamilyFinder()
: PT_FamilyFinder
- PT_FF_comImpl()
: PT_FF_comImpl
- PT_selection()
: PT_selection
- PT_statistic()
: PT_statistic
- PT_Traversal()
: PT_Traversal
- ptnd_chain_count_mishits()
: ptnd_chain_count_mishits
- PTserverConnection()
: PTserverConnection
- push()
: ALI_TSTACK< T >
, AP_STACK< ELEM >
, PARSIMONY_testenv< SEQTYPE >
, SearchFIFO
- push_back()
: JoinedLocation
- push_clip_scale()
: AW_device
- push_node()
: AP_main
- push_transaction()
: AWT_canvas
, GB_MAIN_TYPE
- push_whole_tree()
: PARSIMONY_testenv< SEQTYPE >
- put()
: BufferPtr< T >
, ConstStrArray
, FINAL_TYPE< SEQTYPE >
, GBS_strstruct
, LineBuf
, Memory
, output
, PS_FileBuffer
, ResourceStack
, SPOOLER
- put_artificial_part()
: PartRegistry
- put_before()
: ConstStrArray
, FINAL_TYPE< SEQTYPE >
- put_char()
: PS_FileBuffer
- put_entry()
: MO_Liste
- put_int()
: PS_FileBuffer
- put_long()
: PS_FileBuffer
- put_part_from_complete_tree()
: PartRegistry
- put_part_from_partial_tree()
: PartRegistry
- put_SAI()
: ALI_ARBDB
- put_sequence()
: ALI_ARBDB
- put_sequence_string()
: ALI_ARBDB
- put_Sonde()
: Sondentopf
- put_uint()
: PS_FileBuffer
- put_ulong()
: PS_FileBuffer
- putColor()
: SPOOLER
- putDefaultColor()
: SPOOLER
- putfloat()
: GBS_strstruct
- putlong()
: GBS_strstruct