Here is a list of all file members with links to the files they belong to:

- s -

s : AW_awar.cxx
S_fp : f2c.h
SAFE_EDITING : ED4_edit_string.cxx
safe_write() : AW_status.cxx
safeCharIndex() : dupstr.h
SafeSize() : glpng.c
SAI : RNA3D_StructureData.hxx
sai_assert : SaiProbeVisualization.hxx , saiop.h
SAI_CLR_COUNT : SaiProbeVisualization.hxx
SAI_COUNTED_CHARS : ad_spec.cxx
SAI_GC_0 : SaiProbeVisualization.hxx
SAI_GC_1 : SaiProbeVisualization.hxx
SAI_GC_2 : SaiProbeVisualization.hxx
SAI_GC_3 : SaiProbeVisualization.hxx
SAI_GC_4 : SaiProbeVisualization.hxx
SAI_GC_5 : SaiProbeVisualization.hxx
SAI_GC_6 : SaiProbeVisualization.hxx
SAI_GC_7 : SaiProbeVisualization.hxx
SAI_GC_8 : SaiProbeVisualization.hxx
SAI_GC_9 : SaiProbeVisualization.hxx
SAI_GC_FOREGROUND : SaiProbeVisualization.hxx
SAI_GC_FOREGROUND_FONT : SaiProbeVisualization.hxx
SAI_GC_HIGHLIGHT : SaiProbeVisualization.hxx
SAI_GC_HIGHLIGHT_FONT : SaiProbeVisualization.hxx
SAI_GC_MAX : SaiProbeVisualization.hxx
SAI_GC_PROBE : SaiProbeVisualization.hxx
SAI_GC_PROBE_FONT : SaiProbeVisualization.hxx
SAI_get_selector() : items.h , SAIs.cxx
sai_group_sel : ad_ext.cxx
SAI_init_calculator_awars() : saicalc.cxx
SAI_OPERATOR_TYPES : saiop.h
SAI_popup_calculator_window() : saicalc.cxx , saicalc.h
sai_seletion_changed_cb() : saicalc.cxx
sai_transtab_awar() : ED4_visualizeSAI.cxx
SaiAliScope : calculator.h
SaiBoolOp : saiop.h
SaiBoolRulePtr : saiop.h
saicalc_config_mapping : saicalc.cxx
saicalc_edit_method_cb() : saicalc.cxx
saicalc_predefined_configs : saicalc.cxx
saiChanged_callback() : ED4_visualizeSAI.cxx
SAICOLORS : RNA3D_StructureData.cxx
SaiContains : NT_ins_col.cxx
saiHasDataInAli() : calculator.cxx
SaiOperatorPtr : saiop.h
SaiOperatorType : saiop.h
saiValues : SaiProbeVisualization.cxx
SAS_ALL : calculator.h
SAS_COMMON : calculator.h
SAS_SELECTED : calculator.h
SAS_TARGET : calculator.h
SAVE : db_query.cxx
save_cb() : AWT_config_manager.cxx
save_comments() : AWT_config_manager.cxx
save_list_cb() : AWT_sel_boxes.cxx
save_lower_subtree() : PT_buildtree.cxx
save_messagebox_content_to() : AW_status.cxx
save_probe_collection() : probe_design.cxx
save_probe_list_to_DB() : probe_design.cxx
save_results() : DI_clusters.cxx
save_results_recursive() : DI_clusters.cxx
save_search_paras_to_file() : ED4_search.cxx
save_tree_as_newick() : arb_consensus_tree.cxx
save_upper_tree() : PT_buildtree.cxx
saveArb() : arb_dnarates.cxx
saveChangedRuleset() : xfergui.cxx
savemode : db_server.cxx
SBO_AND : saiop.h
SBO_FIRST : saiop.h
SBO_NAND : saiop.h
SBO_NOR : saiop.h
SBO_OR : saiop.h
SBO_XNOR : saiop.h
SBO_XOR : saiop.h
SCALE_LENGTH : TreeDisplay.cxx
SCALE_LENGTH_PRESERVING : TreeDisplay.cxx
SCALE_SPREAD : TreeDisplay.cxx
scaleAndRound() : AW_xfig.cxx
ScaleMode : TreeDisplay.cxx
SCALER_MAX_VALUE : AW_button.cxx
SCALER_MIN_VALUE : AW_button.cxx
SCALER_SIZE : DI_view_matrix.cxx
SCALER_WIDTH : TreeDisplay.cxx
scalerChanged_cb() : AW_button.cxx
SCAN_ALL_FIELDS : xfergui.h
scan_bool_parameter() : AWT_input_mask.cxx
scan_existing_input_masks() : AWT_input_mask.cxx
scan_flag_parameter() : AWT_input_mask.cxx
scan_gene_positions() : arb_gene_probe.cxx
scan_identifier() : AWT_input_mask.cxx
SCAN_INPUT_FIELDS : xfergui.h
scan_keyword_parameter() : AWT_input_mask.cxx
scan_long_parameter() : AWT_input_mask.cxx
scan_optional_parameter() : AWT_input_mask.cxx
SCAN_OUTPUT_FIELDS : xfergui.h
scan_string_or_keyword_parameter() : AWT_input_mask.cxx
scan_string_parameter() : AWT_input_mask.cxx
scan_token() : prototypes.h , util.cxx
scan_token_or_die() : prototypes.h , util.cxx
scanGbdByKey() : admap.cxx
scanKeywords() : readcfg.c
scanMinIndentation() : arb_help2xml.cxx
scanned_existing_input_masks : AWT_input_mask.cxx
scanner_dst : MG_species.cxx
scanner_src : MG_species.cxx
scanSeqlenFromID() : Importer.cxx
scanSeqlenFromLOCUS() : Importer.cxx
scanToken() : SEC_main.cxx
Score : align.cxx
SCORE_LEFT : fast_aligner.cxx
SCORE_RIGHT : fast_aligner.cxx
screen2printer() : AW_print.cxx
screen_update_callback : awt_canvas.hxx
screenGamma : glpng.c
script_part_of() : nds.cxx
scroll_hor_cb() : AWT_canvas.cxx
scroll_sellist() : AW_button.cxx
scroll_sellist_dn() : AW_button.cxx
scroll_sellist_up() : AW_button.cxx
scroll_vert_cb() : AWT_canvas.cxx
scrollHalfPage() : ED4_no_class.cxx
SEARCH : RNA3D_StructureData.hxx
search__ATTR__ : mkptypes.cxx
SEARCH_ALL_TREES : NT_group_search.cxx
SEARCH_BROTHER : arbdb.h
SEARCH_CHILD : arbdb.h
SEARCH_CHILD_OF_NEXT : arbdb.h
search_comment_for_attribute() : mkptypes.cxx
search_comment_for_promotion() : mkptypes.cxx
SEARCH_CURRENT_TREE : NT_group_search.cxx
SEARCH_GRANDCHILD : arbdb.h
SEARCH_NEXT_BROTHER : arbdb.h
search_params_changed_action : ED4_search.cxx
SEARCH_PATTERNS : ed4_search.hxx
SEARCH_SELECTED_TREES : NT_group_search.cxx
search_window_map : ED4_search.cxx
SearchedTreeContainer : group_search.cxx
SearchedTreeIter : group_search.cxx
searchParamsChanged() : ED4_search.cxx
searchWord() : adoptimize.cxx
SEC : arb_sleep.h
sec2disp() : AW_status.cxx
SEC_ANY_TYPE : SEC_root.hxx
sec_assert : SEC_defs.hxx
SEC_BASE_TYPE : SEC_root.hxx
SEC_bgpaint_mode : SEC_root.hxx
SEC_BUGS : arb_help2xml.cxx
SEC_center_cb() : SEC_main.cxx
SEC_create_bonddef_window() : SEC_main.cxx
SEC_create_display_window() : SEC_main.cxx
SEC_create_gc_window() : SEC_main.cxx
sec_dbcb() : SEC_db.cxx
SEC_delete_structure() : SEC_main.cxx
SEC_DESCRIPTION : arb_help2xml.cxx
SEC_EXAMPLES : arb_help2xml.cxx
SEC_exit() : SEC_main.cxx
sec_expect_closing_bracket() : SEC_read.cxx
sec_expect_constraints() : SEC_read.cxx
sec_expect_keyword_and_doubles() : SEC_read.cxx
sec_expect_keyword_and_ints() : SEC_read.cxx
SEC_FAKE : arb_help2xml.cxx
SEC_fit_window_cb() : SEC_main.cxx
SEC_foldedHelixList_to_xstring() : SEC_helix.cxx , SEC_helix.hxx
SEC_GC_BONDS : SEC_gc.hxx
SEC_GC_CBACK_0 : SEC_gc.hxx
SEC_GC_CBACK_1 : SEC_gc.hxx
SEC_GC_CBACK_2 : SEC_gc.hxx
SEC_GC_CBACK_3 : SEC_gc.hxx
SEC_GC_CBACK_4 : SEC_gc.hxx
SEC_GC_CBACK_5 : SEC_gc.hxx
SEC_GC_CBACK_6 : SEC_gc.hxx
SEC_GC_CBACK_7 : SEC_gc.hxx
SEC_GC_CBACK_8 : SEC_gc.hxx
SEC_GC_CBACK_9 : SEC_gc.hxx
SEC_GC_CURSOR : SEC_gc.hxx
SEC_GC_DATA_COUNT : SEC_gc.hxx
SEC_GC_DEFAULT : SEC_gc.hxx
SEC_GC_ECOLI : SEC_gc.hxx
SEC_GC_ERROR : SEC_gc.hxx
SEC_GC_FIRST_DATA : SEC_gc.hxx
SEC_GC_FIRST_FONT : SEC_gc.hxx
SEC_GC_FONT_COUNT : SEC_gc.hxx
SEC_GC_HELIX : SEC_gc.hxx
SEC_GC_HELIX_NO : SEC_gc.hxx
SEC_GC_LAST_DATA : SEC_gc.hxx
SEC_GC_LAST_FONT : SEC_gc.hxx
SEC_GC_LOOP : SEC_gc.hxx
SEC_GC_MAX : SEC_gc.hxx
SEC_GC_MBACK : SEC_gc.hxx
SEC_GC_NHELIX : SEC_gc.hxx
SEC_GC_SBACK_0 : SEC_gc.hxx
SEC_GC_SBACK_1 : SEC_gc.hxx
SEC_GC_SBACK_2 : SEC_gc.hxx
SEC_GC_SBACK_3 : SEC_gc.hxx
SEC_GC_SBACK_4 : SEC_gc.hxx
SEC_GC_SBACK_5 : SEC_gc.hxx
SEC_GC_SBACK_6 : SEC_gc.hxx
SEC_GC_SBACK_7 : SEC_gc.hxx
SEC_GC_SBACK_8 : SEC_gc.hxx
SEC_HELIX : SEC_root.hxx
SEC_importExport() : SEC_main.cxx
SEC_is_gap() : SEC_root.hxx
SEC_LINE_WIDTH : AWT_input_mask.cxx
SEC_LOOP : SEC_root.hxx
sec_mode_event() : SEC_main.cxx
SEC_new_structure() : SEC_main.cxx
SEC_NO_TYPE : SEC_root.hxx
SEC_NONE : arb_help2xml.cxx
SEC_NOTES : arb_help2xml.cxx
SEC_OCCURRENCE : arb_help2xml.cxx
sec_read_line() : SEC_read.cxx
SEC_rename_structure() : SEC_main.cxx
sec_scan_doubles() : SEC_read.cxx
sec_scan_ints() : SEC_read.cxx
SEC_SECTION : arb_help2xml.cxx
SEC_SKELE_HELIX : SEC_gc.hxx
SEC_SKELE_LOOP : SEC_gc.hxx
SEC_SKELE_NHELIX : SEC_gc.hxx
SEC_structure_changed_cb() : SEC_graphic.cxx
SEC_sync_colors() : SEC_main.cxx
SEC_toggle_cb() : SEC_main.cxx
SEC_undo_cb() : SEC_main.cxx
SEC_UPDATE_OK : SEC_graphic.hxx
SEC_UPDATE_RECOUNT : SEC_graphic.hxx
SEC_UPDATE_RELOAD : SEC_graphic.hxx
SEC_update_request : SEC_graphic.hxx
SEC_UPDATE_SHOWN_POSITIONS : SEC_graphic.hxx
SEC_WARNINGS : arb_help2xml.cxx
SEC_XBORDER : AWT_input_mask.cxx
SEC_xstring_to_foldedHelixList() : SEC_helix.cxx , SEC_helix.hxx
SEC_YBORDER : AWT_input_mask.cxx
secedit_display_config_mapping : SEC_main.cxx
SECOND : arb_perf_test.cxx , UnitTester.cxx
SECONDS : UnitTester.hxx
secS() : align.cxx
SECSTRUCT_SECSTRUCT : ed4_protein_2nd_structure.hxx
SECSTRUCT_SEQUENCE : ed4_protein_2nd_structure.hxx
SECSTRUCT_SEQUENCE_PREDICT : ed4_protein_2nd_structure.hxx
SectionList : arb_help2xml.cxx
SectionType : arb_help2xml.cxx
seen_corrupt_data : ad_save_load.cxx
seen_valgrinded_call() : ut_valgrinded.h
SEG_MAX : SEC_structure.cxx
SEL_CLUSTER : DI_clusters.cxx
sel_isort_backward() : AW_select.cxx
sel_sort_backward() : AW_select.cxx
SELBOX_AUTOREFRESH_FREQUENCY : AW_file.cxx
selbox_install_autorefresh() : AW_file.cxx
select_cluster() : DI_clusters.cxx
select_cluster_cb() : DI_clusters.cxx
select_named_sequence_terminal() : ED4_cursor.cxx
select_organism() : species.cxx
select_reference() : MG_preserves.cxx
select_representative() : DI_clusters.cxx
select_SAI() : SAIs.cxx
select_species() : species.cxx
SelectableFields : item_sel_list.h
SELECTED : NT_ins_col.cxx
SELECTED_BAD_ALI : ED4_detect_bad_ali.cxx
selected_changed_cb() : ED4_detect_bad_ali.cxx
selected_config_changed_cb() : NT_edconf.cxx
selected_configs_awar_changed_cb() : NT_edconf.cxx
selected_configs_display_awar_changed_cb() : NT_edconf.cxx
selected_configs_list : NT_edconf.cxx
SELECTED_FIELD : AWT_config_manager.cxx
selected_field_changed_cb() : AWT_config_manager.cxx
selected_fts_changed_cb() : xfergui.cxx
selected_fts_file_changed() : xfergui.cxx
selected_group_changed_by_canvas_cb() : NT_group_search.cxx
selected_list : MP_Window.cxx , MultiProbe.hxx
selected_match_changed_cb() : probe_design.cxx
selected_probe_changed_cb() : probe_design.cxx
selected_rule_changed_cb() : xfergui.cxx
SELECTED_SPECIES : ED4_detect_bad_ali.cxx
selected_species_changed_cb() : DI_view_matrix.cxx
selected_tree_changed_cb() : DI_matr.cxx
SelectedAwar : ED4_detect_bad_ali.cxx
selectedSpeciesChanged_cb() : NT_extern.cxx
selectLowerIslands() : align.cxx
selectMnemonic() : AWT_input_mask.cxx
selectRule() : xfergui.cxx
selectUpperIslands() : align.cxx
selectValidNameFromList() : NT_validManual.cxx
sellist_cmp_fun : aw_select.hxx
sellist_update_cb : aw_select.hxx
SEP : xferset.cxx
SEPARATOR : mpdefs.h
seq : rns.c , rns.h
seq_array : ClustalV.cxx
seq_assert : SQ_ambiguities.h , SQ_GroupData.h , SQ_physical_layout.h
SEQ_CHARS : seq_search.hxx
seq_color_awars_created : ED4_seq_colors.cxx
SEQ_COLOR_SET_ELEMS : ED4_seq_colors.cxx
SEQ_COLOR_SETS : ED4_seq_colors.cxx
seq_colors_changed_cb() : ED4_main.cxx
SEQ_POINT : ed4_edit_string.hxx
seq_quality_config_mapping : SQ_main.cxx
SEQ_TERM_TEXT_YOFFSET : ed4_defs.hxx , ED4_main.cxx
seqchecksum : ureadseq.h
seqFileFormat() : ureadseq.c , ureadseq.h
seqFileFormatFp() : ureadseq.c , ureadseq.h
seqlen_array : ClustalV.cxx
SEQLINE : defs.h
SeqPtr : seq.h
seqsymbols : ureadseq.c
SEQUENCE : AP_buffer.hxx
sequence_changed_cb() : ED4_base.cxx
sequence_info_terminal_spec : ED4_terminal.cxx
SEQUENCE_INFO_WIDTH : ed4_defs.hxx
sequence_is_partial() : TreeCallbacks.cxx
sequence_manager_spec : ED4_manager.cxx
sequence_terminal_spec : ED4_terminal.cxx
SER : AP_seq_simple_pro.hxx
serve_db_interrupt() : dbserver.cxx
served() : db_server.cxx
SERVER_ERROR : adcomm.cxx
server_load() : names.cxx
server_main_loop() : db_server.cxx
SERVER_RECEIVE_ERROR : adcomm.cxx
server_save() : names.cxx
SERVER_SEND_ERROR : adcomm.cxx
server_shutdown() : names.cxx , PT_main.cxx , pt_prototypes.h
SERVER_VERSION : names.cxx
ServerMode : ali_pt.hxx
set_addid() : AW_rename.cxx
set_advice_id() : AW_advice.cxx
set_all_modules_to() : TestEnvironment.cxx
set_and_realloc_gde_array() : ED4_main.cxx
set_autoselect_cb() : ED4_visualizeSAI.cxx
set_col_stat_activated_and_refresh() : ED4_colStat.cxx
set_constant_fields() : GDE_arbdb_io.cxx
set_current_as_diffRef() : ED4_seq_colors.cxx
set_DB_state() : PT_main.cxx
set_diff_reference() : ED4_seq_colors.cxx
set_displ() : ClustalV.cxx
set_display_update_callback() : GEN_map.cxx
set_empty_addids() : names.cxx
set_extract_common() : AP_buffer.cxx
set_father() : probe_tree.h
set_field_of_queried_cb() : db_query.cxx
set_focus_policy() : AW_root.cxx
SET_GB_DATA_LIST_HEADER() : gb_data.h
SET_GB_ENTRIES_ENTRY : gb_index.h
SET_GB_FATHER() : gb_data.h
SET_GB_HEADER_LIST_GBD() : gb_header.h
SET_GB_IF_ENTRIES_GBD() : gb_index.h
SET_GB_IF_ENTRIES_NEXT() : gb_index.h
SET_GB_INDEX_FILES_ENTRIES() : gb_index.h
SET_GB_INDEX_FILES_NEXT() : gb_index.h
SET_GBCONTAINER_ELEM() : gb_header.h
SET_GBCONTAINER_IFS() : gb_index.h
set_global_option() : arb_a2ps.c
set_intEntry_to() : adtools.cxx
set_keep_ghostnodes() : PARS_main.cxx
set_mag_from_psize() : AWT_canio.cxx
set_marks_of() : group_search.cxx
set_masters_with_sons() : adseqcompr.cxx
set_max() : PT_match.cxx
set_paper_size_xy() : AWT_canio.cxx
set_parents_with_only_temp_childs_temp() : AW_root.cxx
set_positional_option() : arb_a2ps.c
set_protection_level() : ad_load.cxx
set_protection_of_queried_cb() : db_query.cxx
SET_QUERIED() : db_query.cxx
set_result_bit : GEN_translations.cxx
set_SAI_group() : ad_ext.cxx
set_SAI_group_cb() : ad_ext.cxx
set_selected_FTS() : xfergui.cxx
set_suffix() : AW_file.cxx
set_tree_idx() : adtree.cxx
set_type() : probe_tree.h
setCfgError() : readcfg.c , readcfg.h
setIntEntryToZero() : trackers.cxx
setMinMax() : AW_xfig.cxx
setOrAppendQualifiedEntry() : Feature.cxx
SetParams() : glpng.c
SetTime() : GDE_Genbank.cxx , GDE_proto.h
settingName() : ED4_flags.cxx
settings : ED4_search.cxx
SETUP : TestEnvironment.cxx
setup_configmarker_config_cb() : NT_edconf.cxx
setup_gde_config_def() : GDE.cxx
setup_helix_config() : AW_helix.cxx
setup_keymap_config() : AWT_map_key.cxx
setup_modify_fields_config() : db_query.cxx
setup_next_neighbour_config() : ui_species.cxx
setup_pfold_config() : ED4_protein_2nd_structure.cxx
setup_probe_config() : probe_design.cxx
setup_saiColorDefs_config() : SaiProbeVisualization.cxx
setup_search_config() : ED4_search.cxx
setup_species_flags_config() : ED4_flags.cxx
setupnodex() : arb_dnarates.cxx
setuptree() : arb_dnarates.cxx
setupxarray() : arb_dnarates.cxx
setVisualizeSAI_cb() : ED4_visualizeSAI.cxx
setVisualizeSAI_options_cb() : ED4_visualizeSAI.cxx
SF_ALLOW_NEW : item_sel_list.h
SF_HIDDEN : item_sel_list.h
SF_PSEUDO : item_sel_list.h
SF_SHOW_TYPE : item_sel_list.h
SF_STANDARD : item_sel_list.h
ShadedValue : item_shader.h
ShaderPluginPtr : item_shader.h
Shaders : item_shader.cxx
shall_store_in_config() : GDE.cxx
SHAPE_MAX : RNA3D_Textures.hxx
SHAPES : RNA3D_Renderer.hxx
sheets : arb_a2ps.c
sheetside : arb_a2ps.c
shell_manager : arbdb.cxx
SHIFT_ARGS : arb_read_tree.cxx , arb_write_tree_comment.cxx
SHIFT_NONSWITCHES : arb_read_tree.cxx , arb_write_tree_comment.cxx
shiftKeyIsDown() : macinit.c
short : ureadseq.h
SHORT_CHAIN_HEADER_ELEMS : probe_tree.h
SHORT_CHAIN_HEADER_FLAG_BIT : probe_tree.h
SHORT_CHAIN_HEADER_SIZE_MASK : probe_tree.h
SHORT_TABLE_ELEM_SIZE : chartable.h
SHORT_TABLE_MAX_VALUE : chartable.h
shortenLongString() : gb_aci.cxx
shortenString() : ED4_search.cxx
shortint : f2c.h
SHORTLEN_DECR : adoptimize.cxx
shortlogical : f2c.h
shorttimecopy() : reader.h
shorttimekeep() : reader.h
shouldReflow() : arb_help2xml.cxx
SHOW_ABS_CURPOS : SEC_root.hxx
show_all_changekeys() : changekey.cxx
SHOW_BASE_CURPOS : SEC_root.hxx
show_command_line_usage() : main.cxx
show_count() : TreeCallbacks.cxx
show_detailed_column_stats_activated() : ED4_colStat.cxx
SHOW_ECOLI_CURPOS : SEC_root.hxx
show_err() : arb_help2xml.cxx
show_error() : arb_read_tree.cxx , arb_write_tree_comment.cxx
show_error_and_warnings() : arb_help2xml.cxx
SHOW_HELIX_BONDS : SEC_root.hxx
show_help() : db_server.cxx
show_message() : arb_read_tree.cxx , arb_write_tree_comment.cxx
SHOW_NHELIX_BONDS : SEC_root.hxx
SHOW_NO_BONDS : SEC_root.hxx
SHOW_NO_CURPOS : SEC_root.hxx
show_probes_in_sellist() : probe_design.cxx
show_sina_window() : graph_aligner_gui.cxx , graph_aligner_gui.hxx
show_soft_link() : AW_file.cxx
show_tracked_error() : AW_inotify.cxx
show_usage() : arb_sub2ascii.cxx
show_warning() : arb_help2xml.cxx
show_warnings() : arb_help2xml.cxx
ShowBonds : SEC_root.hxx
ShowCursorPos : SEC_root.hxx
showDeconstructingSubtitle() : SyncRoot.cxx
showhelp : arb_probe.cxx
shown_apos() : PT_new_design.cxx
SHOWN_CLUSTERS : di_foundclusters.hxx
shown_ecoli() : PT_new_design.cxx
shown_qual() : PT_new_design.cxx
ShowVendorInformation() : RNA3D_OpenGLEngine.cxx
shutdown_macro_recording() : macros.hxx , trackers.cxx
SigHandler : SigHandler.h
SIGMATRUNCATION_CONST : MultiProbe.hxx
SIGNIFICANT_FIELD_CHARS : ED4_no_class.cxx
sigsegv_handler() : arb_signal.cxx
sigsegv_occurred : server.c
SIMILARITY : di_protdist.hxx
SIMPLE_RESHADE : item_shader.h
SIMPLE_TYPE : arb_proto_2_xsub.cxx
sina_cmd_changed_cb() : graph_aligner_gui.cxx
sina_config_mapping : graph_aligner_gui.cxx
sina_mask() : graph_aligner_gui.cxx , graph_aligner_gui.hxx
sina_select_ref_db() : graph_aligner_gui.cxx
sina_start() : graph_aligner_gui.cxx
SinaArbInterfaceVersion : graph_aligner_gui.cxx
single2full_dtree() : adoptimize.cxx
SINGLE_COLUMNS : insdel.h
SINGLE_NODE : adoptimize.cxx
SingleBuffer : RNA3D_OpenGLEngine.cxx
SingleProb : rns.h
sio_assert : seqio.cxx , seq_export.cxx
sitecombcrunch() : arb_dnarates.cxx
sites : arb_dnarates.cxx
sitesort() : arb_dnarates.cxx
SIZE : date.cxx
SIZE_AUTHORITY : GDE_def.h
SIZE_DESCRIPTION : GDE_def.h
SIZE_FIELD_GENBANK : GDE_def.h
SIZE_ID : GDE_def.h
SIZE_MASK : PT_prefixtree.cxx
SIZE_SEQ_NAME : GDE_def.h
SIZE_SHORT_NAME : GDE_def.h
SizedReadBuffer : TranslateRealign.cxx
SizedWriteBuffer : TranslateRealign.cxx
sizetarray2string() : GEN_interface.cxx
SIZOFINTERN : gb_data.h
SKIP_COLUMN_IF_MAX : phylo.hxx
SKIP_COLUMN_IF_OCCUR : phylo.hxx
skip_eolnl_and_append() : prototypes.h , util.cxx
skip_eolnl_and_append_spaced() : prototypes.h , util.cxx
SKIP_FOLDED_EDGES : pars_awars.h
SKIP_INNER_EDGES : pars_awars.h
SKIP_LEAF_EDGES : pars_awars.h
skip_page() : arb_a2ps.c
skip_pattern() : prototypes.h , util.cxx
SKIP_SPACE_LF() : aisc_inline.h
SKIP_SPACE_LF_BACKWARD() : aisc_inline.h
skip_strain() : prototypes.h , util.cxx
skip_subspecies() : prototypes.h , util.cxx
SKIP_TMP_PREFIX : item_shader.cxx
SKIP_UNMARKED_EDGES : pars_awars.h
Skip_white_space() : prototypes.h , util.cxx
skipit() : mkptypes.cxx
skipwhitespace : ureadseq.h
slave_gap_extend() : ClustalV.cxx
slave_gap_open() : ClustalV.cxx
slave_gapAt() : ClustalV.cxx
slave_gapAtWithOpenPenalty() : ClustalV.cxx
sleepms() : UnitTester.cxx , UnitTester.hxx
SLIDER : GDE_def.h
SLIDER_OFFSET : ed4_defs.hxx
SLIDERFIELDWIDTH : GDE.cxx
SLIDERWIDTH : GDE.cxx
SLOW_is_pseudo_key() : db_query.cxx
SM_ANY : admatch.cxx
SM_INVALID : admatch.cxx
SM_REGEXPR : admatch.cxx
SM_WILDCARDED : admatch.cxx
SmartArrayPtr : smartptr.h
SmartCustomPtr : smartptr.h , CT_common.hxx , DBwriter.cxx
SmartMallocPtr() : gb_aci.h , smartptr.h
snd_list : ClustalV.cxx
softbaseiter : MG_adapt_ali.cxx
softbaselist : MG_adapt_ali.cxx
SOP_ACI : saiop.h
SOP_BOOLCHAIN : saiop.h
SOP_MATRIX : saiop.h
SOP_TRANSLATE : saiop.h
SORT_ALPHA : AW_file.cxx
SORT_BY_CLUSTERSIZE : di_foundclusters.hxx
SORT_BY_MAX_DIST : di_foundclusters.hxx
SORT_BY_MEANDIST : di_foundclusters.hxx
SORT_BY_MIN_BASES : di_foundclusters.hxx
SORT_BY_MIN_DIST : di_foundclusters.hxx
SORT_BY_MISMATCHES : arb_probe_match.cxx
SORT_BY_TREEPOSITION : di_foundclusters.hxx
SORT_BY_TYPE : arb_probe_match.cxx
SORT_BY_WEIGHTED_MISMATCHES : arb_probe_match.cxx
SORT_BY_WEIGHTED_MISMATCHES_W_POS_AND_STRENGTH : arb_probe_match.cxx
SORT_DATE : AW_file.cxx
sort_dict_offsets() : adoptimize.cxx
sort_dtree_by_other_tree_cb() : ad_trees.cxx
sort_gbdata_offsets() : admap.cxx
sort_keys() : ui_species.cxx
sort_order_changed_cb() : DI_clusters.cxx
SORT_REVERSE : di_foundclusters.hxx
sort_sequences_by_length() : PARS_main.cxx
SORT_SIZE : AW_file.cxx
sort_tprobes_by() : PT_new_design.cxx
sort_tree_by_other_tree() : ad_trees.cxx
sort_tree_by_other_tree_cb() : ad_trees.cxx
SortCriteria : group_search.h
sorted_primes : adhash.cxx
SortedPairValues : DI_clustertree.cxx
SortedPositions : ScrollSynchronizer.cxx
sortOldestFirst() : AP_tree_nlen.cxx
SOURCE : xferset.cxx
SOURCE_ADMIN : AliAdmin.h
source_sai_list_changed_cb() : saicalc.cxx
SPACE_BEHIND_BUTTON : aw_varupdate.hxx
SPACE_BEHIND_LABEL : AW_button.cxx
SPACED : MP_Window.cxx
spaced_weightable() : arb_progress.cxx
SPACER_HEIGHT : ed4_defs.hxx
SPACER_NOCONS_HEIGHT : ed4_defs.hxx
spacer_terminal_spec : ED4_terminal.cxx
spanSubtree() : arb_dnarates.cxx
SPAWN_ASYNCHRONOUS : servercntrl.h
SPAWN_DAEMONIZED : servercntrl.h
SpawnMode : servercntrl.h
Species2Tip : DI_clusters.cxx
species_callback : arbdbt.h
species_copy_cb() : ui_species.cxx
species_create_cb() : ui_species.cxx
species_create_handler() : ui_species.cxx
species_delete_cb() : ui_species.cxx
species_field_selection_list_rescan() : changekey.cxx , item_sel_list.h
species_field_selection_list_unhide_all_cb() : changekey.cxx , item_sel_list.h
species_field_selection_list_update_cb() : changekey.cxx , item_sel_list.h
SPECIES_get_selector() : items.h , species.cxx
species_has_alignment() : TreeCallbacks.cxx
species_iterator : SQ_functions.cxx
species_manager_spec : ED4_manager.cxx
SPECIES_NAME_LEN : PH_display.hxx
species_name_terminal_spec : ED4_terminal.cxx
species_not_found() : fast_aligner.cxx
species_rename_cb() : ui_species.cxx
species_rename_handler() : ui_species.cxx
species_rename_join() : NT_join.cxx
species_requires() : probe_design.cxx
SpeciesCreationMode : ed4_class.hxx
SpeciesFlagCiter : ed4_flags.hxx
SpeciesFlagIter : ed4_flags.hxx
SpeciesFlagList : ed4_flags.hxx
SpeciesID : ps_defs.hxx
SpeciesMergeListLength() : ED4_no_class.cxx
SpeciesNames : group_search.h
speciesOrOrganism() : items.h
SpeciesPositions : ScrollSynchronizer.cxx
SpeciesSet : ScrollSynchronizer.h
SpeciesSetPtr : ScrollSynchronizer.h
SpeciesXferScope : MG_species.cxx
SpeciesXferType : MG_species.cxx
SPECIFIED_OBJECT_TYPES : ed4_class.hxx
SpecifiedMode : ali_pt.hxx
SpinMolecule() : RNA3D_Interface.cxx
split_ali_cb() : NT_split_ali.cxx
split_alignment() : NT_split_ali.cxx
split_data_into_parts() : NT_split_ali.cxx
SPLIT_DROPEMPTY : arb_strarray.h
split_gene_counter : arb_gene_probe.cxx
SPLIT_KEEPEMPTY : arb_strarray.h
split_sort_mask() : db_query.cxx
split_stat_filename() : ColumnStat_2_gnuplot.cxx
splitEmblTag() : Importer.cxx
splitEntry() : GDE_ParseMenu.cxx
splitGenebankTag() : Importer.cxx
SplitMode : arb_strarray.h
splitRate : rns.c , rns.h
splitRNS() : rns.h , rns.c
splits_for_match_overlay : PT_match.cxx
splitTokComment() : ED4_search.cxx
SpoolablePtr : AW_print.cxx
spoolColor : AW_print.cxx
spoolDefaultColor : AW_print.cxx
spoolf : AW_print.cxx
spools : AW_print.cxx
Spreading : spreadin.h
spreadRand() : spreadin.c , spreadin.h
SQ_add_changekeys() : SQ_functions.cxx
sq_calc_seq_quality_cb() : SQ_main.cxx
SQ_check_tree_structure() : SQ_functions.cxx , SQ_functions.h
SQ_clear_group_dictionary() : SQ_functions.h , SQ_functions.cxx
SQ_create_awars() : SQ_main.cxx , seq_quality.h
SQ_create_seq_quality_window() : SQ_main.cxx , seq_quality.h
SQ_evaluate() : SQ_functions.cxx , SQ_functions.h
SQ_fetch_filtered_sequence() : SQ_functions.cxx
SQ_GroupDataDictionary : SQ_functions.h
SQ_GroupDataPtr : SQ_functions.h
SQ_mark_species() : SQ_functions.cxx , SQ_functions.h
SQ_pass1() : SQ_functions.cxx
SQ_pass1_no_tree() : SQ_functions.h , SQ_functions.cxx
SQ_pass1_on_tree() : SQ_functions.h , SQ_functions.cxx
SQ_pass2() : SQ_functions.cxx
SQ_pass2_no_tree() : SQ_functions.cxx , SQ_functions.h
SQ_pass2_on_tree() : SQ_functions.cxx , SQ_functions.h
SQ_remove_quality_entries() : SQ_functions.h , SQ_functions.cxx
sq_remove_quality_entries_cb() : SQ_main.cxx
sq_round() : SQ_functions.cxx
SQ_TREE_ERROR : SQ_functions.h
squarepyramidal_number() : triangular.h
SRC_DB : merge.hxx
SRT_AUTOCORRECT_ALINAME : arbdbt.h
SRT_AUTOCORRECT_TREENAME : arbdbt.h
SRT_AWARCOLSTAT_ALIGNMENT : ColumnStat.cxx
SRT_AWARCOLSTAT_ENABLE_HELIX : ColumnStat.cxx
SRT_AWARCOLSTAT_NAME : ColumnStat.cxx
SRT_AWARCOLSTAT_SMOOTH : ColumnStat.cxx
ssl_from_storage : awt_sel_boxes.hxx
ssl_to_storage : awt_sel_boxes.hxx
SSU_16S : RNA3D_StructureData.hxx
ST_A : st_ml.hxx
st_assert : st_quality.hxx , st_ml.hxx
ST_BUCKET_SIZE : MostLikelySeq.hxx
ST_C : st_ml.hxx
st_check_cb() : ST_window.cxx
ST_FLOAT : st_ml.hxx
ST_G : st_ml.hxx
ST_GAP : st_ml.hxx
ST_MAX_BASE : st_ml.hxx
ST_MAX_SEQ_PART : MostLikelySeq.hxx
st_ml : ed4_class.hxx
st_ml_add_quality_string_to_species() : ST_quality.cxx
st_ml_add_sequence_part_to_stat() : ST_quality.cxx
ST_ML_AWAR : ST_window.cxx
ST_ML_AWAR_COLSTAT_NAME : ST_window.cxx
ST_ML_AWAR_COLSTAT_PREFIX : ST_window.cxx
ST_ML_AWAR_CQ_BUCKET_SIZE : ST_window.cxx
ST_ML_AWAR_CQ_DEST_FIELD : ST_window.cxx
ST_ML_AWAR_CQ_KEEP_REPORTS : ST_window.cxx
ST_ML_AWAR_CQ_MARKED_ONLY : ST_window.cxx
ST_ML_AWAR_CQ_REPORT : ST_window.cxx
ST_ML_AWAR_FILTER_ALIGNMENT : ST_window.cxx
ST_ML_AWAR_FILTER_FILTER : ST_window.cxx
ST_ML_AWAR_FILTER_NAME : ST_window.cxx
ST_ML_AWAR_FILTER_PREFIX : ST_window.cxx
ST_ML_AWAR_FILTER_SIMPLIFY : ST_window.cxx
st_ml_check_sequence_quality() : ST_quality.cxx , st_quality.hxx
ST_ML_Color : st_ml.hxx , st_window.hxx
st_ok_cb() : ST_window.cxx
ST_QUALITY_REPORT_NONE : st_window.hxx
ST_QUALITY_REPORT_TEMP : st_window.hxx
ST_QUALITY_REPORT_YES : st_window.hxx
st_remove_entries() : ST_window.cxx
st_remove_entries_cb() : ST_window.cxx
st_report_enum : st_window.hxx
st_sequence_callback() : ST_ml.cxx
st_sequence_del_callback() : ST_ml.cxx
ST_T : st_ml.hxx
ST_UNDEFINED : AW_Xm.cxx
ST_UNKNOWN : st_ml.hxx
STACKSIZE : aisc_def.h
Stage : probe.h
STAGE1 : probe.h
STAGE1_BYTES_PER_BASE : PT_partition.h
STAGE1_BYTES_PER_PASS_OLIGO : PT_partition.h
STAGE1_EXTRA_MB : PT_partition.h
STAGE1_INDEX_BYTES_PER_BASE : PT_partition.h
STAGE1_INDEX_BYTES_PER_PASS_OLIGO : PT_partition.h
STAGE1_INDEX_EXTRA_MB : PT_partition.h
STAGE1_OTHER_BYTES_PER_BASE : PT_partition.h
STAGE1_OTHER_BYTES_PER_PASS_OLIGO : PT_partition.h
STAGE1_OTHER_EXTRA_MB : PT_partition.h
STAGE2 : probe.h
STANDARD : defs.h
STANDARD_CALL : aisc_commands.c
standard_file2list() : AWT_sel_boxes.cxx
standard_list2file() : AWT_sel_boxes.cxx
STANDARD_PADDING : awt_canvas.hxx
StandardOrientation : glpng.c
STAR : RNA3D_Textures.hxx
STAR_SMOOTH : RNA3D_Textures.hxx
start : RNA3D_StructureData.cxx
start2D : RNA3D_StructureData.cxx
start2D3D : RNA3D_StructureData.cxx
start3D : RNA3D_StructureData.cxx
start_macro_cb() : macro_gui.cxx
start_main_window_after_import() : NT_main.cxx
start_of_main() : arb_main.h
start_pt_server() : PT_main.cxx
start_remote_command_for_application() : adtools.cxx
start_RNA3D_plugin() : RNA3D_Main.cxx , rna3d_extern.hxx
start_SECEDIT_plugin() : SEC_main.cxx , secedit_extern.hxx
startIns : RNA3D_StructureData.cxx
startpage() : arb_a2ps.c
startSp : RNA3D_StructureData.cxx
startsWithLetter() : arb_help2xml.cxx
startsWithNumber() : arb_help2xml.cxx
startTime : PT_main.cxx
startup_dbserver() : dbserver.hxx , dbserver.cxx
startup_gui() : NT_main.cxx
startup_mainwindow_and_dbserver() : NT_main.cxx
startup_merge_main_window() : NT_main.cxx
startup_merge_prompting_for_nonexplicit_dbs() : NT_main.cxx
startup_merge_prompting_for_nonexplicit_dst_db() : NT_main.cxx
startup_sequence_cb() : PH_main.cxx
stat2display() : ED4_terminal.cxx
STAT_create_awars() : ST_window.cxx
STAT_create_chimera_check_window() : st_window.hxx , ST_window.cxx
STAT_create_main_window() : ST_window.cxx , st_window.hxx
STAT_create_ST_ML() : st_window.hxx , ST_window.cxx
STAT_destroy_ST_ML() : st_window.hxx , ST_window.cxx
STAT_find_node_by_name() : st_window.hxx , ST_window.cxx
STAT_get_color_string() : st_window.hxx , ST_window.cxx
STAT_set_postcalc_callback() : st_window.hxx , ST_window.cxx
STAT_update_ml_likelihood() : ST_window.cxx , st_window.hxx
STATIC_ASSERT() : probe_tree.h , db_scanner.cxx , ED4_seq_colors.cxx , arb_pathlen.h , ED4_seq_colors.cxx , probe_tree.h , arb_help2xml.cxx , DI_matr.cxx , adseqcompr.cxx , arb_pathlen.h , static_assert.h , probe_tree.h , AP_seq_protein.cxx , arb_pathlen.h , PT_prefixtree.cxx , probe_tree.h , ED4_objspec.cxx , AP_seq_protein.cxx , AW_xfont.cxx , cb.cxx , AW_preset.cxx , PT_tools.h , AW_preset.cxx , AW_xfont.cxx
STATIC_ASSERT_ANNOTATED() : arb_early_check.h , static_assert.h , arbdb.cxx , AW_window.cxx
STATIC_BUFFER() : ad_save_load.cxx
static_downcast() : downcast.h
static_error : arb_diff.cxx
static_pntr : ARB_ext.c
status : arb_handlers.cxx
STATUS_PREFIX : NT_dbrepair.cxx
status_started : AW_status.cxx
status_write_cmd_and_text() : AW_status.cxx
StatusCommand : AW_status.cxx
STD_LABEL_LEN : AW_preset.cxx
StdGetFile() : macinit.c
stdsymbols : ureadseq.c
StencilBlue : glpng.c
StencilGreen : glpng.c
StencilRed : glpng.c
Step : ps_my2asciipaths.cxx
STEPS : ED4_cursor.cxx
STIPPLE_TYPES : AW_Xm.cxx
StippleType : AW_Xm.cxx
STOP : AP_seq_simple_pro.hxx
stop_in_debugger : arb_assert.h
StopKey() : macinit.c
store_cb() : AWT_config_manager.cxx
store_clusters() : DI_clusters.cxx
store_gene_species_xfer_fields() : MG_gene_species.cxx
store_generated_config_cb() : AWT_config_manager.cxx
store_inside_entry() : gb_storage.h
store_selected_cluster() : DI_clusters.cxx
store_unused_detached_info_window_cb() : info_window.cxx
STORED_CLUSTERS : di_foundclusters.hxx
STORED_COMMENTS : AWT_config_manager.cxx
str : defines.h
str0len() : global.h
str2pattern() : ED4_search.cxx
str_equal() : global.h
str_iequal() : global.h
StrArray_FROM_HELIXLIST : ED4_detect_bad_ali.cxx
Strcasecmp() : ureadseq.h , ureadseq.c
strcasecmp_start() : main.cxx
strcpy_truncate() : GDE_def.h
strcpydest() : MG_gene_species.cxx
strdup_getlen() : AW_window.cxx
strduplen() : aisc_inline.h
stream2static() : graph_aligner_gui.cxx
streamIntFunResults() : test_helpers.h
streamIntFunResultsInBrackets() : test_helpers.h
strf() : util.cxx , prototypes.h
strict_resort_data_base() : NT_sort.cxx
string() : arb_help2xml.cxx
string2enum() : adperl.cxx
string2enum_or_die() : adperl.cxx
string2PlotType() : ColumnStat_2_gnuplot.cxx
string2WordSet() : group_search.cxx
string_comparator() : mkptypes.cxx
string_matcher_type : admatch.cxx
string_to_lower() : group_search.cxx
stringize : stringize.h
stringize_pscan : stringize.h
stringMap : Location.h , types.h
StringSet : NT_dbrepair.cxx
stringSet : types.h
stringVector : types.h
StringVector : saicalc.cxx , ED4_detect_bad_ali.cxx
StripSpecial() : GDE_HGLfile.cxx
stristr() : prototypes.h , util.cxx
strlwr() : PH_filt.cxx
Strncasecmp() : ureadseq.h , ureadseq.c
strndup() : global.h
strpartdup() : probe_match_parser.cxx
StrSet : xfergui.cxx
StrSetIter : xfergui.cxx
STRUCT_BAD_MATCH : ed4_protein_2nd_structure.hxx
STRUCT_GOOD_MATCH : ed4_protein_2nd_structure.hxx
STRUCT_MEDIUM_MATCH : ed4_protein_2nd_structure.hxx
STRUCT_NO_MATCH : ed4_protein_2nd_structure.hxx
STRUCT_PERFECT_MATCH : ed4_protein_2nd_structure.hxx
STRUCT_UNKNOWN : ed4_protein_2nd_structure.hxx
STRUCTURE : AP_buffer.hxx
STRUCTURE_BACKBONE : RNA3D_StructureData.hxx
STRUCTURE_BACKBONE_CLR : RNA3D_StructureData.hxx
structure_breaker : ED4_protein_2nd_structure.cxx
structure_chars : ED4_protein_2nd_structure.cxx
structure_indifferent : ED4_protein_2nd_structure.cxx
STRUCTURE_POS : RNA3D_StructureData.hxx
STRUCTURE_POS_ANCHOR : RNA3D_StructureData.hxx
STRUCTURE_SUMMARY : ed4_protein_2nd_structure.hxx
SUBSET_NOELEM_DISPLAY : AWT_sel_boxes.cxx
SubsetChangedCb : awt_sel_boxes.hxx
subtract_sons_from_tree() : adseqcompr.cxx
subtreeLength() : arb_dnarates.cxx
sum_of_triangular_numbers() : triangular.h
summarize() : arb_dnarates.cxx
Supp : align.cxx
SUPPORTED_COMPRESSION_FLAGS : ad_save_load.cxx
supported_sina_versions : graph_aligner_gui.cxx
suppress_sigsegv : arb_signal.cxx
svd_() : eispack.cxx
swap() : ad_io_inline.h , adoptimize.cxx , adGene.cxx , admap.cxx
swap_clusters() : DI_clusters.cxx
swap_configs() : NT_edconf.cxx
swap_source_dest_cb() : ad_trees.cxx
SWISSPROT : fun.h
SXS_LISTED_SPECIES : MG_species.cxx
SXS_SELECTED_SPECIES : MG_species.cxx
SXT_SINGLE_FIELD : MG_species.cxx
SXT_USING_FTS : MG_species.cxx
SXT_USING_FTS_SKIP_ALI : MG_species.cxx
SXT_WHOLE_SPECIES : MG_species.cxx
sync_changed_cb() : NT_sync_scroll.cxx
SyncColors : SEC_main.cxx
SynchronizeColorsWithEditor() : RNA3D_Interface.cxx
synchronizer : NT_sync_scroll.cxx
system3_tab : MultiProbe.hxx , MP_noclass.cxx
system3_tab_size : MP_noclass.cxx