- p -
- p_encode()
: ClustalV.cxx
- page_size_check_cb()
: AWT_canio.cxx
- paintBackgroundAndSAI()
: SaiProbeVisualization.cxx
- paintProbeInfo()
: SaiProbeVisualization.cxx
- paper_changed_cb()
: AWT_canio.cxx
- paren_string()
: mg.cxx
- parentEdge()
: TreeNode.h
- pars_check_size()
: PARS_main.cxx
- pars_create_all_awars()
: PARS_main.cxx
- pars_exit()
: PARS_main.cxx
- pars_generate_aliview()
: PARS_dtree.cxx
- PARS_infomode_cb()
: PARS_main.cxx
- PARS_map_viewer()
: PARS_main.cxx
, pars_main.hxx
- pars_reset_optimal_parsimony()
: PARS_main.cxx
- pars_start_cb()
: PARS_main.cxx
- PARS_tree_init()
: PARS_dtree.cxx
, pars_dtree.hxx
- parse_CMD_RADIO()
: AWT_input_mask.cxx
- parse_env_mem_definition()
: adsocket.cxx
- parse_helix_list()
: ED4_detect_bad_ali.cxx
- parse_intype()
: main.cxx
- parse_key_word()
: prototypes.h
, util.cxx
- parse_names_into_gene_struct()
: PT_main.cxx
- parse_outtype()
: main.cxx
- parse_quoted_string()
: recmac.cxx
- parse_RDP_comment()
: prototypes.h
, rdp_info.cxx
- parse_remark()
: TreeNode.h
- parse_treelabel()
: TreeNode.h
- parse_type()
: main.cxx
- parseCommandLine()
: arb_probe.cxx
- parseCounter()
: Importer.cxx
- parseCSV()
: adGene.cxx
- parseFontString()
: AW_xfont.cxx
- parseformat()
: readseq.c
- parseInfix()
: Location.cxx
- parseLocation()
: Location.cxx
, Location.h
- parseLocationList()
: Location.cxx
- ParseMenus()
: GDE_ParseMenu.cxx
- parsePosition()
: Location.cxx
- parsePositions()
: adGene.cxx
- parseSection()
: arb_help2xml.cxx
- parsesize()
: AW_xfont.cxx
- part2SimpleLocation()
: Location.cxx
- part_of()
: client.c
- partial_mtoe()
: embl.cxx
- partof()
: insdel.cxx
- partSignificance()
: fast_aligner.cxx
- pattern2str()
: ED4_search.cxx
- paup_print_header()
: paup.cxx
- paup_print_header_counters()
: paup.cxx
- paup_print_headerstart()
: paup.cxx
- paup_print_line()
: paup.cxx
- paup_verify_name()
: paup.cxx
- pd_edit_ptserver_log()
: probe_design.cxx
- pd_export_pt_server()
: probe_design.cxx
- pd_get_the_gene_names()
: probe_design.cxx
- pd_get_the_names()
: probe_design.cxx
- pd_kill_pt_server()
: probe_design.cxx
- pd_query_pt_server()
: probe_design.cxx
- pd_start_pt_server()
: probe_design.cxx
- pd_view_server_console()
: probe_design.cxx
- PELEM_cmp()
: CT_part.cxx
- percentMarked()
: TreeDisplay.cxx
- perform_block_operation_on_part_of_sequence()
: ED4_block.cxx
- perform_block_operation_on_whole_sequence()
: ED4_block.cxx
- perform_query_cb()
: db_query.cxx
- performmode_relative_id()
: GEN_map.cxx
- permutations()
: group_search.cxx
- PG_get_first_probe()
: ps_pg_tree_functions.hxx
- PG_get_next_probe()
: ps_pg_tree_functions.hxx
- PG_initSpeciesMaps()
: ps_pg_specmap.hxx
- PG_NumberSpecies()
: ps_pg_specmap.hxx
- PG_read_probe()
: ps_pg_tree_functions.hxx
- PG_SpeciesID2SpeciesName()
: ps_pg_specmap.hxx
- PG_SpeciesName2SpeciesID()
: ps_pg_specmap.hxx
- ph_calc_filter_cb()
: PH_display.cxx
, PH_display.hxx
- ph_check_initialized()
: PH_display.cxx
, PH_display.hxx
- PH_create_filter_variables()
: PH_filt.cxx
, phylo.hxx
- PH_create_filter_window()
: PH_filt.cxx
, phylo.hxx
- PH_create_ml_multiline_SAI()
: PH_main.cxx
- ph_exit()
: PH_main.cxx
- PH_save_markerline()
: PH_main.cxx
- PH_save_ml_cb()
: PH_main.cxx
- PH_save_ml_multiline_cb()
: PH_main.cxx
- PH_timer()
: PH_filt.cxx
- ph_view_species_cb()
: PH_display.cxx
, PH_display.hxx
- phylip_print_line()
: phylip.cxx
- pixmapPath()
: AW_button.cxx
- plural()
: arb_string.h
- pngBind()
: glpng.c
, glpng.h
- pngLoad()
: glpng.c
- pngLoadF()
: glpng.c
- polygon_contains()
: AW_device_click.cxx
- popdown_search_window_cb()
: NT_group_search.cxx
- popup_detached_experiment_window()
: EXP_interface.cxx
- popup_detached_gene_window()
: GEN_interface.cxx
- popup_detached_speciesOrganismWindow()
: ui_species.cxx
- popup_field_selection()
: item_sel_list.cxx
- popup_gene_location_editor()
: GEN_interface.cxx
- popup_group_clusters_window()
: DI_clusters.cxx
- popup_group_search_window()
: NT_group_search.cxx
, NT_group_search.h
- popup_interrupt_macro_window_cb()
: macro_gui.cxx
- popup_macro_window()
: macro_gui.cxx
- popup_match_window_cb()
: probe_design.cxx
- popup_new_experiment_window()
: EXP_interface.cxx
- popup_new_gene_window()
: GEN_interface.cxx
- popup_new_main_window()
: NT_extern.cxx
- popup_new_speciesOrganismWindow()
: ui_species.cxx
- popup_probe_design_result_window()
: probe_design.cxx
- popup_rule_definition_window()
: xfergui.cxx
- popup_ruleset_admin_window()
: xfergui.cxx
- popup_SelectionListSpec_cb()
: AWT_sel_boxes.cxx
- popup_single_field_transfer_window()
: MG_species.cxx
- popup_speciesOrganismWindow()
: ui_species.cxx
- popup_tree_admin_window()
: ad_trees.cxx
, ad_trees.h
- popupSaiProbeMatchWindow()
: probe_design.cxx
- PRD_strdup()
: PRD_Item.cxx
- preCreateTempfile()
: GDE_event.cxx
- predef_prg()
: db_query.cxx
- preferredForCommand()
: TreeDisplay.cxx
- prefix_before()
: arb_proto_2_xsub.cxx
- prepare_and_get_selected_itemfield()
: item_sel_list.cxx
, item_sel_list.h
- primer_design_event_check_gc_factor()
: primer_design.cxx
- primer_design_event_check_primer_length()
: primer_design.cxx
- primer_design_event_check_temp_factor()
: primer_design.cxx
- primer_design_event_go()
: primer_design.cxx
- primer_design_event_init()
: primer_design.cxx
- primer_design_event_update_memory()
: primer_design.cxx
- primer_print()
: arb_primer.cxx
- print_file()
: arb_a2ps.c
- print_man()
: ali_main.cxx
- print_page_prologue()
: arb_a2ps.c
- print_pos()
: AW_print.cxx
- print_prologue()
: arb_a2ps.c
- print_promotions()
: mkptypes.cxx
- print_prototype_parse_error()
: arb_proto_2_xsub.cxx
- print_standard_prologue()
: arb_a2ps.c
- print_tabs()
: aisc_commands.c
- print_XML_Text_expanding_links()
: arb_help2xml.cxx
- print_xs_default()
: arb_proto_2_xsub.cxx
- printable_print_line()
: printable.cxx
- printchar()
: arb_a2ps.c
- printFile()
: AWT_asciiprint.cxx
- printpage()
: arb_a2ps.c
- probe_2_readable()
: probe.h
- probe_collection_close()
: probe_design.cxx
- probe_collection_load_prompt()
: probe_design.cxx
- probe_collection_save_prompt()
: probe_design.cxx
- probe_collection_update_parameters()
: probe_design.cxx
- probe_common_send_data()
: probe_design.cxx
- probe_compress_sequence()
: PT_io.cxx
, pt_prototypes.h
- probe_design_event()
: probe_design.cxx
- probe_design_send_data()
: probe_design.cxx
- probe_forget_matches_event()
: probe_design.cxx
- probe_match()
: PT_match.cxx
, pt_prototypes.h
- probe_match_all_event()
: probe_design.cxx
- probe_match_event()
: probe_design.cxx
- probe_match_event_using_awars()
: probe_design.cxx
- probe_match_send_data()
: probe_design.cxx
- probe_match_update_probe_list()
: probe_design.cxx
- probe_match_with_specificity_edit_event()
: probe_design.cxx
- probe_match_with_specificity_enum_callback()
: probe_design.cxx
- probe_match_with_specificity_event()
: probe_design.cxx
- probe_read_data_base()
: PT_io.cxx
, pt_prototypes.h
- probelength_changed_cb()
: probe_design.cxx
- processLength()
: arb_dnarates.cxx
- propertyName()
: ED4_root.cxx
- protect_corruption_error()
: ad_save_load.cxx
- protMatches()
: AP_codon_table.cxx
- provide_insDelBuffer()
: insdel.cxx
- PS_apply_path_to_bitmap()
: ps_find_probes.cxx
- PS_ascend()
: ps_find_probes.cxx
- PS_assert_inverse_path()
: ps_convert_db.cxx
- PS_assert_path()
: ps_convert_db.cxx
- PS_calc_min_sum_of_square_distances_to_average()
: ps_eval_candidates.cxx
- PS_calc_next_speciesid_sets()
: ps_find_probes.cxx
- PS_calc_sums_for_nodepath()
: ps_eval_candidates.cxx
- PS_calc_temp()
: ps_eval_candidates.cxx
- PS_descend()
: ps_find_probes.cxx
- PS_detect_probe_length()
: ps_convert_db.cxx
- PS_detect_weak_differences()
: ps_detect_weak_differences.cxx
- PS_detect_weak_differences_stepdown()
: ps_detect_weak_differences.cxx
- PS_eval_node_paths()
: ps_eval_candidates.cxx
- PS_extract_probe_data()
: ps_convert_db.cxx
- PS_filling_level()
: ps_find_probes.cxx
- PS_find_probe_for_sets()
: ps_find_probes.cxx
- PS_find_probes()
: ps_find_probes.cxx
- PS_find_probes_for_pairs()
: ps_detect_weak_differences.cxx
- PS_get_first_node()
: ps_pg_tree_functions.hxx
- PS_get_leaf_candidates()
: ps_eval_candidates.cxx
, ps_find_probes.cxx
- PS_get_next_candidates()
: ps_find_probes.cxx
- PS_get_next_candidates_descend()
: ps_find_probes.cxx
- PS_get_next_node()
: ps_pg_tree_functions.hxx
- PS_get_node_paths()
: ps_eval_candidates.cxx
- PS_get_probe_for_path()
: ps_get_probes.cxx
- PS_GNUPlot()
: ps_find_probes.cxx
- PS_make_map_for_candidate()
: ps_find_probes.cxx
- PS_print_and_evaluate_map()
: ps_detect_weak_differences.cxx
- PS_print_map_ranges()
: ps_find_probes.cxx
- PS_print_paths()
: ps_arb2asciipaths.cxx
, ps_my2asciipaths.cxx
- PS_print_set_ranges()
: ps_find_probes.cxx
- PS_print_time_diff()
: ps_tools.cxx
, ps_tools.hxx
- PS_printProbe()
: ps_node.hxx
- PS_remove_bad_probes()
: ps_eval_candidates.cxx
- PS_test_candidate_on_bitmap()
: ps_find_probes.cxx
- PS_test_sets_on_path()
: ps_find_probes.cxx
- pseudo_species_hash_key()
: adGene.cxx
- PT_abs_2_ecoli_rel()
: PT_io.cxx
, pt_prototypes.h
- PT_add_to_chain()
: PT_prefixtree.cxx
, pt_prototypes.h
- pt_build_pos_to_weight()
: PT_match.cxx
- PT_build_species_hash()
: PT_io.cxx
, pt_prototypes.h
- PT_chain_has_valid_entries()
: pt_prototypes.h
, PT_prefixtree.cxx
- PT_change_leaf_to_node()
: PT_prefixtree.cxx
, pt_prototypes.h
- PT_change_link_in_father()
: PT_prefixtree.cxx
- PT_create_leaf()
: PT_prefixtree.cxx
, pt_prototypes.h
- pt_destroy_locs()
: PT_extern.c
- pt_destroy_socket()
: PT_extern.c
- PT_dump_POS_TREE()
: PT_debug.cxx
, pt_prototypes.h
- PT_dump_POS_TREE_recursive()
: PT_debug.cxx
, pt_prototypes.h
- PT_dump_POS_TREE_to_file()
: PT_debug.cxx
- PT_dump_tree_statistics()
: PT_debug.cxx
, pt_prototypes.h
- PT_exit()
: PT_main.cxx
- PT_exit_psg()
: pt_prototypes.h
, PT_main.cxx
- pt_export_error()
: PT_etc.cxx
, pt_prototypes.h
- pt_export_error_if()
: pt_prototypes.h
, PT_etc.cxx
- PT_find_exProb()
: PT_findEx.cxx
, pt_prototypes.h
- PT_forwhole_chain()
: probe_tree.h
, pt_prototypes.h
, probe_tree.h
, pt_prototypes.h
, probe_tree.h
- pt_get_gc_content()
: PT_new_design.cxx
- pt_get_temperature()
: PT_new_design.cxx
- PT_index_dump()
: PT_debug.cxx
, pt_prototypes.h
- pt_init_bond_matrix()
: PT_new_design.cxx
, pt_prototypes.h
, PT_extern.c
- PT_init_cache_sizes()
: pt_prototypes.h
, PT_prefixtree.cxx
- PT_init_input_data()
: PT_io.cxx
, pt_prototypes.h
- pt_init_main_struct()
: PT_main.cxx
- PT_init_map()
: PT_main.cxx
- PT_init_psg()
: pt_prototypes.h
, PT_main.cxx
- pt_init_socket()
: PT_extern.c
- PT_leaf_size()
: probe_tree.h
- PT_leaf_to_chain()
: PT_prefixtree.cxx
, pt_prototypes.h
- PT_node_size()
: probe_tree.h
- PT_prepare_data()
: PT_io.cxx
, pt_prototypes.h
- PT_prepare_species_sequence()
: PT_io.cxx
- PT_read_big()
: PT_tools.h
- PT_READ_CHAIN_ENTRY_stage_2()
: probe_tree.h
- PT_read_char()
: PT_tools.h
- PT_read_compact_nat()
: PT_tools.h
- PT_read_int()
: PT_tools.h
- PT_read_pointer()
: PT_tools.h
- PT_read_short()
: PT_tools.h
- PT_read_son()
: probe_tree.h
- PT_read_son< POS_TREE1 >()
: probe_tree.h
- PT_read_son< POS_TREE2 >()
: probe_tree.h
- PT_read_void_pointer()
: PT_tools.h
- pt_sort_compare_match()
: PT_match.cxx
- pt_sort_match_list()
: PT_match.cxx
- PT_start_design()
: PT_new_design.cxx
, pt_prototypes.h
- PT_unknown_names()
: PT_etc.cxx
, pt_prototypes.h
- PT_write_big()
: PT_tools.h
- PT_WRITE_CHAIN_ENTRY()
: probe_tree.h
- PT_write_char()
: PT_tools.h
- PT_write_compact_nat()
: PT_tools.h
- PT_write_int()
: PT_tools.h
- PT_write_pointer()
: PT_tools.h
- PT_write_short()
: PT_tools.h
- PTD_debug_nodes()
: pt_prototypes.h
- PTD_delete_saved_node()
: pt_prototypes.h
, PT_prefixtree.cxx
- PTD_put_byte()
: pt_prototypes.h
, PT_prefixtree.cxx
- PTD_put_int()
: pt_prototypes.h
, PT_prefixtree.cxx
- PTD_put_longlong()
: pt_prototypes.h
- PTD_put_short()
: PT_prefixtree.cxx
, pt_prototypes.h
- PTD_read_leafs_from_disk()
: pt_prototypes.h
, PT_prefixtree.cxx
- PTD_save_lower_tree()
: pt_prototypes.h
, PT_buildtree.cxx
- PTD_save_upper_tree()
: pt_prototypes.h
, PT_buildtree.cxx
- PTD_set_object_to_saved_status()
: PT_prefixtree.cxx
- PTD_write_chain_to_disk()
: PT_prefixtree.cxx
- PTD_write_leafs_to_disk()
: pt_prototypes.h
, PT_prefixtree.cxx
- PTD_write_node_to_disk()
: PT_prefixtree.cxx
- PTD_write_tip_to_disk()
: PT_prefixtree.cxx
- ptnd_compare_quality()
: PT_new_design.cxx
- ptnd_compare_sequence()
: PT_new_design.cxx
- ptpd_read_names()
: PT_etc.cxx
, pt_prototypes.h
- ptserver()
: TestEnvironment.cxx
- ptserver_directory_info_command()
: probe_design.cxx
- ptserver_gene()
: TestEnvironment.cxx
- ptserverlog_changed_cb()
: AWT_sel_boxes.cxx
- push_all_upnode_sequences()
: AP_tree_nlen.cxx
- push_partial()
: PARS_main.cxx
- pushParagraph()
: arb_help2xml.cxx
- put_compact_nat()
: PT_prefixtree.cxx
- putelem()
: GDE_arbdb_io.cxx
, GDE_proto.h
- PV_AddCallBacks()
: ED4_ProteinViewer.cxx
- PV_AddCorrespondingOrfTerminals()
: ed4_ProteinViewer.hxx
, ED4_ProteinViewer.cxx
- PV_AddNewAAseqTerminals()
: ED4_ProteinViewer.cxx
- PV_AddOrfTerminalsToLoadedSpecies()
: ED4_ProteinViewer.cxx
, ed4_ProteinViewer.hxx
- PV_CallBackFunction()
: ed4_ProteinViewer.hxx
, ED4_ProteinViewer.cxx
- PV_ComplementarySequence()
: ED4_ProteinViewer.cxx
- PV_CreateAllTerminals()
: ED4_ProteinViewer.cxx
- PV_CreateAwars()
: ED4_ProteinViewer.cxx
, ed4_ProteinViewer.hxx
- PV_DisplayAminoAcidNames()
: ED4_ProteinViewer.cxx
- PV_HideAllTerminals()
: ED4_ProteinViewer.cxx
- PV_HideTerminal()
: ED4_ProteinViewer.cxx
- PV_LookForNewTerminals()
: ED4_ProteinViewer.cxx
- PV_ManageTerminalDisplay()
: ED4_ProteinViewer.cxx
- PV_ManageTerminals()
: ED4_ProteinViewer.cxx
- PV_PrintMissingDBentryInformation()
: ED4_ProteinViewer.cxx
- PV_RefreshDisplay()
: ED4_ProteinViewer.cxx
- PV_RefreshProtViewDisplay()
: ED4_ProteinViewer.cxx
- PV_RefreshWindow()
: ed4_ProteinViewer.hxx
, ED4_ProteinViewer.cxx
- PV_SaveData()
: ED4_ProteinViewer.cxx
- PV_SequenceUpdate_CB()
: ed4_ProteinViewer.hxx
, ED4_ProteinViewer.cxx
- PV_UnHideTerminal()
: ED4_ProteinViewer.cxx
- PV_WriteTranslatedSequenceToDB()
: ED4_ProteinViewer.cxx
- PVP_calculate()
: pvp.h
, pvp.cxx
- pythag_()
: eispack.cxx