- r -
- raise_reference_cb()
: MG_preserves.cxx
- randomMixTree()
: PARS_main.cxx
- randProb()
: frand.h
, frand.c
- randval()
: frand.c
- range_changed_cb()
: NT_ins_col.cxx
- range_contained_in()
: ED4_base.cxx
- range_count_update_cb()
: NT_ins_col.cxx
- range_overlay_changed_cb()
: AW_preset.cxx
- ranges_overlap()
: ED4_base.cxx
- ratqr_()
: eispack.cxx
- RB_INFO_order()
: CT_rbtree.cxx
- react_to_command()
: db_server.cxx
- read_accession_file()
: arb_export_sequences.cxx
- read_aisc_file()
: aisc_proto.h
, aisc.c
- read_alignment()
: prototypes.h
, seq.cxx
- read_export_format()
: seq_export.cxx
- read_import_format()
: AWTI_import.cxx
- read_int_with_reserved_bits()
: PT_tools.h
- read_keyword()
: ad_load.cxx
- read_mapping_awar()
: AWT_map_key.cxx
- read_name()
: fast_aligner.cxx
- read_nat_with_reserved_bits()
: PT_tools.h
- read_references()
: MG_preserves.cxx
- read_sequence_region()
: ui_species.cxx
- read_tree_and_size_internal()
: adtree.cxx
- readable_combined_protein()
: AP_seq_protein.cxx
- readable_probe()
: PT_io.cxx
, pt_prototypes.h
- readable_pt_servername()
: AWT_sel_boxes.cxx
- readableItemname()
: GDE_ParseMenu.cxx
- readableTime()
: AW_status.cxx
- readableUnknownNames()
: probe_design.cxx
- readACC()
: GEN_map.cxx
- readAndWrite()
: adoptimize.cxx
- ReadArbdb()
: GDE_arbdb_io.cxx
, GDE_proto.h
- ReadArbdb2()
: GDE_arbdb_io.cxx
, GDE_proto.h
- readCfg()
: readcfg.c
, readcfg.h
- readCmdOptions()
: macinit.c
- readCompactedSequence()
: fast_aligner.cxx
- readEMBL()
: ureadseq.c
- readFirstCompressedDataOf()
: NT_dbrepair.cxx
- readFitch()
: ureadseq.c
- ReadGen()
: GDE_Genbank.cxx
, GDE_proto.h
- readGenBank()
: ureadseq.c
- readIG()
: ureadseq.c
- readLine()
: AWT_input_mask.cxx
- readline()
: ureadseq.c
- readLoop()
: ureadseq.c
- readMSF()
: ureadseq.c
- ReadNA_Flat()
: GDE_FileIO.cxx
- readNBRF()
: ureadseq.c
- readOlsen()
: ureadseq.c
- readopt()
: readseq.c
- readPAUPinterleaved()
: ureadseq.c
- readPAUPsequential()
: ureadseq.c
- readPearson()
: ureadseq.c
- readPhylipInterleaved()
: ureadseq.c
- readPhylipSequential()
: ureadseq.c
- readPIR()
: ureadseq.c
- readPlain()
: ureadseq.c
- readSeq()
: ureadseq.c
, ureadseq.h
- readSeqFp()
: ureadseq.c
, ureadseq.h
- readSeqMain()
: ureadseq.c
- readSimCfg()
: simcfg.c
, simcfg.h
- readStrider()
: ureadseq.c
- readUWGCG()
: ureadseq.c
- readXmlTree()
: ad_trees.cxx
- readZuker()
: ureadseq.c
- realign_event()
: ad_transpro.cxx
- Realize()
: GLwDrawA.c
- realloc_unleaked()
: aisc_interpreter.h
- really_exit()
: NT_extern.cxx
- rebak_()
: eispack.cxx
- rebakb_()
: eispack.cxx
- rebuild_consensus()
: ed4_class.hxx
, ED4_no_class.cxx
- rebuild_rule_from_awars_cb()
: xfergui.cxx
- reconfigure_dbserver()
: dbserver.cxx
, dbserver.hxx
- record_state_changed_cb()
: trackers.cxx
- rect_corner()
: AW_clipable.cxx
- recursiveNNI()
: PARS_main.cxx
- redisplay_needed()
: DI_view_matrix.cxx
- Redraw()
: GLwDrawA.c
- redraw_cursor()
: ED4_main.cxx
- reduc2_()
: eispack.cxx
- reduc_()
: eispack.cxx
- refdata_changed_cb()
: ED4_seq_colors.cxx
- refdata_deleted_cb()
: ED4_seq_colors.cxx
- refDbModeChanged_cb()
: graph_aligner_gui.cxx
- refill_boolrules_sellist()
: saicalc.cxx
- refill_boolrules_sellist_from_AWAR()
: saicalc.cxx
- refill_syncWithList_cb()
: NT_sync_scroll.cxx
- refresh_available_fields_from_ruleset()
: xfergui.cxx
- refresh_availfield_selbox_cb()
: xfergui.cxx
- refresh_columnstat_selection()
: ColumnStat.cxx
- refresh_config_sellist_cb()
: AWT_config_manager.cxx
- refresh_display_cb()
: ED4_visualizeSAI.cxx
- refresh_displayed_experiments()
: EXP_interface.cxx
- refresh_displayed_genes()
: GEN_interface.cxx
- refresh_displayed_SAI()
: SAIs.cxx
- refresh_displayed_species()
: species.cxx
- refresh_fts_selbox()
: xfergui.cxx
- refresh_group_cb()
: ad_ext.cxx
- refresh_grouplist()
: ad_ext.cxx
- refresh_highlighted()
: ED4_block.cxx
- refresh_inputfield_selbox_cb()
: xfergui.cxx
- refresh_matchedProbesDisplay_cb()
: probe_design.cxx
- refresh_reference_list_cb()
: MG_preserves.cxx
- refresh_rule_selection_box_cb()
: xfergui.cxx
- refresh_SAI_groups_cb()
: ad_ext.cxx
- refresh_weights_sellist_cb()
: GDE.cxx
- refresh_without_dbsync()
: MP_noclass.cxx
- refreshCanvas()
: SaiProbeVisualization.cxx
- RefreshCanvas()
: RNA3D_Interface.cxx
- RefreshMappingDisplay()
: RNA3D_Interface.cxx
- RefreshOpenGLDisplay()
: RNA3D_Interface.hxx
, RNA3D_Interface.cxx
- registerIsland()
: align.cxx
- registerItemShader()
: item_shader.cxx
, item_shader.h
- registerType()
: AWT_input_mask.cxx
- Regroup()
: GDE_FileIO.cxx
- reinit_NDS_4_window()
: GEN_map.cxx
- reinit_needed()
: DI_view_matrix.cxx
- relatedBases()
: fast_aligner.cxx
- relative_inside()
: adtools.cxx
- relink_pseudo_species_to_organisms()
: NT_extern.cxx
- relink_tree_rek()
: AP_Tree.cxx
- reload_ecoli_cb()
: ED4_root.cxx
- reload_helix_cb()
: ED4_root.cxx
- remap_scanner_cb()
: AWTI_edit.cxx
- remote_command_handler()
: dbserver.cxx
- remove_advice_id()
: AW_advice.cxx
- remove_by_tab()
: adlang1.cxx
- remove_dup_colors()
: NT_dbrepair.cxx
- remove_for_data_from()
: aisc_commands.c
- remove_from_configs()
: AWT_config_manager.cxx
- remove_from_consensus()
: ED4_terminal.cxx
- remove_hit_cb()
: NT_group_search.cxx
- remove_keydependent_sort_criteria()
: db_query.cxx
- remove_option_from_option_menu()
: AW_option_toggle.cxx
- remove_probe_from_collection_event()
: probe_design.cxx
- remove_redundant_translation()
: GEN_translations.cxx
- remove_tprobes_outside_ecoli_range()
: PT_new_design.cxx
- remove_tprobes_with_too_many_mishits()
: PT_new_design.cxx
- remove_word_from_dtree()
: adoptimize.cxx
- removeFromKnownFields()
: xfergui.cxx
- removeHiddenFiles()
: AWTI_import.cxx
- RemoveQuotes()
: GDE_HGLfile.cxx
- removeSubsequentString()
: adoptimize.cxx
- rename_both_databases()
: MG_names.cxx
- rename_listed_groups_cb()
: NT_group_search.cxx
- rename_SAI_cb()
: ad_ext.cxx
- rename_selected_group_cb()
: NT_group_search.cxx
- renameDB()
: MG_names.cxx
- renameQuicksaves()
: ad_save_load.cxx
- RenderOpenGLScene()
: RNA3D_OpenGLEngine.cxx
, RNA3D_OpenGLEngine.hxx
- reorder_configs_cb()
: NT_edconf.cxx
- reorder_keys()
: ui_species.cxx
- reorder_right_behind_left()
: ui_species.cxx
- reorder_subset_cb()
: AWT_sel_boxes.cxx
- reorder_trees_cb()
: ad_trees.cxx
- reorder_up_down()
: ui_species.cxx
- replace_by_underscore()
: TreeWrite.cxx
- replace_in_block()
: ED4_block.cxx
- ReplaceArgs()
: GDE_event.cxx
- replaceChars()
: ED4_main.cxx
- ReplaceFile()
: GDE_event.cxx
- ReplaceString()
: GDE_event.cxx
- reportSearchPosition()
: ED4_search.cxx
- represents_existing_edge()
: CT_common.hxx
- request_sequence_refresh()
: ED4_root.cxx
- request_terminal_refresh()
: ED4_root.cxx
- rerun_importTest_cb()
: AWTI_edit.cxx
- res_index()
: ClustalV.cxx
- reserve_tree_idx()
: adtree.cxx
- reset_cb()
: AWT_config_manager.cxx
- reset_test_local_flags()
: UnitTester.cxx
- resetFiletype()
: AWT_canio.cxx
- resetGlobals()
: readseq.c
- ReshapeOpenGLWindow()
: RNA3D_OpenGLEngine.hxx
, RNA3D_OpenGLEngine.cxx
- Resize()
: glpng.c
, GLwDrawA.c
- resize_cb()
: PH_main.cxx
- resize_needed()
: DI_view_matrix.cxx
- ResizeOpenGLWindow()
: RNA3D_Interface.cxx
- resolve_IUPAC_target_string()
: probe_design.cxx
- resolved_probe_chosen()
: probe_design.cxx
- resort_data_base()
: NT_sort.cxx
- resort_data_by_customOrder()
: NT_sort.cxx
- restore_cb()
: AWT_config_manager.cxx
- restore_clusters()
: DI_clusters.cxx
- restore_colorset_representation()
: db_query.cxx
- restore_mark()
: aditem.cxx
- result_sort_order_changed_cb()
: db_query.cxx
- result_update_cb()
: group_search.cxx
- resultsAreShown()
: ED4_search.cxx
- reverse_byteorder()
: ad_io_inline.h
- reverse_key_order()
: ui_species.cxx
- reverse_probe()
: probe.h
- reverseColorTranslationTable()
: ED4_visualizeSAI.cxx
- reverseComplement()
: fast_aligner.cxx
- rg_()
: eispack.cxx
- rgg_()
: eispack.cxx
- rightmost_leaf()
: NT_edconf.cxx
- RNA3D_init_global_data()
: RNA3D_Global.hxx
, RNA3D_OpenGLEngine.cxx
- rootEdge()
: ap_main.hxx
, TreeNode.h
- rootNode()
: ap_main.hxx
- rootsync_subsetTrees_vs_selected()
: NT_syncroot.cxx
- RotateMoleculeStateChanged()
: RNA3D_Interface.cxx
- RotateMoleculeStateChanged_cb()
: RNA3D_Interface.cxx
- round_psize()
: AWT_canio.cxx
- rows_changed_cb()
: AWT_canio.cxx
- rs_()
: eispack.cxx
- rs_isdigit()
: readseq.c
- rsb_()
: eispack.cxx
- rsg_()
: eispack.cxx
- rsgab_()
: eispack.cxx
- rsgba_()
: eispack.cxx
- rsm_()
: eispack.cxx
- rsp_()
: eispack.cxx
- rst_()
: eispack.cxx
- rt_()
: eispack.cxx
- rule_stack_cb()
: xfergui.cxx
- ruleSelId()
: xfergui.cxx
- ruleset_awar_changed_cb()
: xfergui.cxx
- run_and_destroy_exit_functions()
: arbdb.cxx
- run_close_callbacks()
: arbdb.cxx
- run_command()
: db_server.cxx
, PT_main.cxx
- run_help_cb()
: AWT_prompt.cxx
- run_rnacma()
: Analyser.cxx
- run_server()
: db_server.cxx
- run_test()
: arb_perf_test.cxx
- runDir()
: TestEnvironment.cxx
- runGroupSearch_cb()
: NT_group_search.cxx
- runtests()
: fb_test.cxx