- 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