- a -

• add() : palign.cpp, palign.c
• add_ggaps() : prfalign.cpp, prfalign.c
• add_ggaps_mask() : prfalign.cpp, prfalign.c
• addinfo() : ureadseq.c
• addrand() : random.cpp, random.c, clustalw.h
• addrandinit() : random.cpp, random.c, clustalw.h
• addseq() : ureadseq.c
• align() : interfac.cpp, interfac.c, clustalw.h
• alloc_aln() : util.cpp, util.c, clustalw.h
• alloc_seq() : util.cpp, util.c, clustalw.h
• aln_score() : clustalw.h, alnscore.cpp, alnscore.c
• avail() : calctree.cpp, calctree.c

- b -

• black_on_white() : xmenu.h
• blank_to_() : util.cpp, util.c, clustalw.h
• blankline() : util.cpp, util.c, clustalw.h
• bootstrap_tree() : trees.cpp, trees.c, clustalw.h

- c -

• calc_colscore() : xmenu.h
• calc_gap_coeff() : clustalw.h, calcgap.cpp, calcgap.c
• calc_gap_penalty_mask() : interfac.cpp, interfac.c
• calc_h_penalties() : calcgap.cpp, calcgap.c
• calc_mean() : calctree.cpp, calctree.c
• calc_p_penalties() : calcgap.cpp, calcgap.c
• calc_percidentity() : interfac.cpp, interfac.c, clustalw.h
• calc_prf1() : clustalw.h, calcprf1.cpp, calcprf1.c
• calc_prf2() : clustalw.h, calcprf2.cpp, calcprf2.c
• calc_root_mean() : calctree.cpp, calctree.c
• calc_score() : palign.cpp, palign.c
• calc_seg_exceptions() : xmenu.h
• calc_segment_exceptions() : xmenu.h
• calc_seq_weights() : clustalw.h, calctree.cpp, calctree.c
• calc_similarities() : clustalw.h, calctree.cpp, calctree.c
• calc_v_penalties() : calcgap.cpp, calcgap.c
• calc_weight() : calctree.cpp, calctree.c
• callback() : TStorage.cpp
• check_dnaflag() : sequence.cpp, sequence.c
• check_infile() : sequence.cpp, sequence.c
• check_menus() : xmenu.h
• check_param() : interfac.cpp, interfac.c
• ckalloc() : util.cpp, util.c, clustalw.h, clustalw.cpp, clustalw.c
• ckfree() : util.cpp, util.c, clustalw.h
• ckrealloc() : util.cpp, util.c, clustalw.h
• cl_blankline() : sequence.cpp, sequence.c
• clear_tree() : clustalw.h, calctree.cpp, calctree.c
• clear_tree_nodes() : calctree.cpp, calctree.c
• clustal_out() : interfac.cpp, interfac.c, clustalw.h
• clustalw_main() : clustalw.cpp, clustalw.c, Alignment.cpp
• cmpint() : main.h, main.cpp
• cmpre() : main.h, main.cpp
• color_prf1() : xmenu.h
• color_prf2() : xmenu.h
• color_seqs() : xmenu.h
• commentline() : readmat.cpp, readmat.c
• compare_tree() : trees.cpp, trees.c
• compressSeq() : ureadseq.h, ureadseq.c
• correct_name_bars() : xmenu.h
• correct_seq_bars() : xmenu.h
• count_clustal_seqs() : sequence.cpp, sequence.c
• count_gaps() : alnscore.cpp, alnscore.c
• count_msf_seqs() : sequence.cpp, sequence.c
• count_pir_seqs() : sequence.cpp, sequence.c
• count_rsf_seqs() : sequence.cpp, sequence.c
• countid() : malign.cpp, malign.c, clustalw.h
• countseq() : ureadseq.c
• CRC32checksum() : ureadseq.h, ureadseq.c
• create_alignment_output() : interfac.cpp, interfac.c, clustalw.h
• create_node() : calctree.cpp, calctree.c
• create_parameter_output() : interfac.cpp, interfac.c
• create_sets() : clustalw.h, calctree.cpp, calctree.c
• create_tree() : calctree.cpp, calctree.c

- d -

• data_colors() : xmenu.h
• del() : palign.cpp, palign.c
• des_quick_sort() : showpair.cpp, showpair.c
• deselect_panel() : xmenu.h
• diff() : palign.cpp, palign.c
• distance_matrix_output() : trees.cpp, trees.c
• dna_distance_matrix() : trees.cpp, trees.c, clustalw.h
• do_system() : util.cpp, util.c, clustalw.h
• draw_allseqs() : xmenu.h
• draw_colscores() : xmenu.h
• draw_footer() : xmenu.h
• draw_header() : xmenu.h
• draw_nameline() : xmenu.h
• draw_names() : xmenu.h
• draw_seq_pointer() : xmenu.h
• draw_seqcol() : xmenu.h
• draw_seqline() : xmenu.h
• draw_seqs() : xmenu.h
• DrawPanel() : xmenu.h

- e -

• endEMBL() : ureadseq.c
• endFitch() : ureadseq.c
• endGB() : ureadseq.c
• endIG() : ureadseq.c
• endNBRF() : ureadseq.c
• endPearson() : ureadseq.c
• endPhylipSequential() : ureadseq.c
• endPIR() : ureadseq.c
• endStrider() : ureadseq.c
• endZuker() : ureadseq.c
• error() : clustalw.h, amenu.cpp, amenu.c
• exit_error() : ncoils.cpp, ncoils.h, ncoils.c, main.h
• explode() : main.h, main.cpp
• ext_penalty1() : prfalign.cpp, prfalign.c
• ext_penalty2() : prfalign.cpp, prfalign.c

- f -

• fast_nj_tree() : trees.cpp, trees.c
• fasta_out() : interfac.cpp, interfac.c, clustalw.h
• fatal() : clustalw.h, amenu.cpp, amenu.c
• fill_chartab() : sequence.cpp, sequence.c, clustalw.h, clustalw.cpp, clustalw.c
• fillrange() : interfac.cpp, interfac.c
• find_file() : xmenu.h
• find_match() : interfac.cpp, interfac.c
• fix_gaps() : interfac.cpp, interfac.c, clustalw.h
• format_options_menu() : amenu.cpp, amenu.c
• forward_pass() : palign.cpp, palign.c
• frag_rel_pos() : showpair.cpp, showpair.c
• free_aln() : util.cpp, util.c, clustalw.h
• free_seq() : util.cpp, util.c, clustalw.h

- g -

• gap_penalties_menu() : amenu.cpp, amenu.c
• gap_penalty1() : prfalign.cpp, prfalign.c
• gap_penalty2() : prfalign.cpp, prfalign.c
• gcg_out() : interfac.cpp, interfac.c, clustalw.h
• GCGchecksum() : ureadseq.h, ureadseq.c
• gde_out() : interfac.cpp, interfac.c, clustalw.h
• get_clustal_seq() : sequence.cpp, sequence.c
• get_clustal_ss() : sequence.cpp, sequence.c
• get_embl_ss() : sequence.cpp, sequence.c
• get_gde_ss() : sequence.cpp, sequence.c
• get_help() : interfac.cpp, interfac.c, clustalw.h
• get_matrix() : readmat.cpp, readmat.c, clustalw.h
• get_msf_seq() : sequence.cpp, sequence.c
• get_path() : util.cpp, util.c, clustalw.h
• get_rsf_feature() : sequence.cpp, sequence.c
• get_rsf_ss() : sequence.cpp, sequence.c
• get_seq() : sequence.cpp, sequence.c
• get_swiss_feature() : sequence.cpp, sequence.c
• get_swiss_mask() : sequence.cpp, sequence.c
• get_tree() : interfac.cpp, interfac.c, clustalw.h
• get_user_matrixname() : xmenu.h
• getargs() : readmat.cpp, readmat.c, clustalw.h
• getint() : util.cpp, util.c, clustalw.h
• getline() : ureadseq.c
• getreal() : util.cpp, util.c, clustalw.h
• getseqtype() : ureadseq.h, ureadseq.c
• getstr() : util.cpp, util.c, clustalw.h
• group_seqs() : calctree.cpp, calctree.c
• guide_tree() : trees.cpp, trees.c, clustalw.h

- h -

• highlight_seqrange() : xmenu.h

- i -

• implode() : main.h, main.cpp
• info() : clustalw.h, amenu.cpp, amenu.c
• init_amenu() : clustalw.h, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c
• init_color_parameters() : xmenu.h
• init_interface() : interfac.cpp, interfac.c, clustalw.h, clustalw.cpp, clustalw.c
• init_matrix() : readmat.cpp, readmat.c, clustalw.h, clustalw.cpp, clustalw.c
• insert_node() : calctree.cpp, calctree.c
• insert_root() : calctree.cpp, calctree.c
• is_ambiguity() : trees.cpp, trees.c
• isAnyChar() : ureadseq.c
• isSeqChar() : ureadseq.c
• isSeqNumChar() : ureadseq.c

- j -

• jumper() : amenu.cpp, amenu.c

- k -

• keyword() : util.cpp, util.c, clustalw.h

- l -

• linetype() : util.cpp, util.c, clustalw.h
• linrand() : random.cpp, random.c, clustalw.h
• listSeqs() : ureadseq.h, ureadseq.c
• load_aln() : xmenu.h
• load_aln_data() : xmenu.h
• local_penalty() : calcgap.cpp, calcgap.c
• lowstr() : util.cpp, util.c, clustalw.h

- m -

• main() : xmltest.cpp, clustalw.h
• main_menu() : clustalw.h, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c
• make_colormask() : xmenu.h
• make_colscores() : xmenu.h
• make_consensus() : xmenu.h
• make_gp_data() : xmenu.h
• make_n_ptrs() : showpair.cpp, showpair.c
• make_p_ptrs() : showpair.cpp, showpair.c
• make_ruler() : xmenu.h
• make_scroll_area() : xmenu.h
• make_struct_data() : xmenu.h
• make_tree() : interfac.cpp, interfac.c, clustalw.h
• malign() : malign.cpp, malign.c, clustalw.h
• mark_group1() : calctree.cpp, calctree.c
• mark_group2() : calctree.cpp, calctree.c
• mult() : random.cpp, random.c
• multi_menu() : amenu.cpp, amenu.c
• multiple_align_menu() : amenu.cpp, amenu.c
• myapp() : main.h, main.cpp

- n -

• n_encode() : sequence.cpp, sequence.c
• nameonly() : interfac.cpp, interfac.c
• nbrf_out() : interfac.cpp, interfac.c, clustalw.h
• ncoils_function() : ncoils.h, ncoils.cpp, ncoils.h, ncoils.c
• ncoils_main() : ncoils.cpp, ncoils.c
• new_sequence_align() : interfac.cpp, interfac.c, clustalw.h
• nexus_out() : interfac.cpp, interfac.c, clustalw.h
• nj_tree() : trees.cpp, trees.c

- o -

• open_alignment_output() : interfac.cpp, interfac.c, clustalw.h
• open_explicit_file() : interfac.cpp, interfac.c, clustalw.h
• open_input_file() : xmenu.h
• open_output_file() : interfac.cpp, interfac.c, clustalw.h
• open_penalty1() : prfalign.cpp, prfalign.c
• open_penalty2() : prfalign.cpp, prfalign.c
• operator<() : TRestrictionEditor.h, TRestrictionEditor.cpp, TProteolysis.h, TProteolysis.cpp, TPrimerDialog.cpp, RestrictionEnzymes.h, RestrictionEnzymes.cpp, MyChild.cpp
• operator<<() : tinyxml.cpp
• operator==() : TRestrictionEditor.h, TRestrictionEditor.cpp, TProteolysis.h, TProteolysis.cpp, TPrimerDialog.cpp, RestrictionEnzymes.h, RestrictionEnzymes.cpp, MyChild.cpp
• order_nodes() : calctree.cpp, calctree.c
• overspill_message() : trees.cpp, trees.c

- p -

• p_encode() : sequence.cpp, sequence.c
• padd() : prfalign.cpp, prfalign.c
• pair_align() : showpair.cpp, showpair.c
• pair_menu() : amenu.cpp, amenu.c
• pairalign() : palign.cpp, palign.c, clustalw.h
• palign() : prfalign.cpp, prfalign.c
• palign1() : malign.cpp, malign.c, clustalw.h
• palign2() : malign.cpp, malign.c, clustalw.h
• parse_params() : interfac.cpp, interfac.c, clustalw.h, clustalw.cpp, clustalw.c
• pdel() : prfalign.cpp, prfalign.c
• pdiff() : prfalign.cpp, prfalign.c
• percentid() : calcgap.cpp, calcgap.c
• phylip_out() : interfac.cpp, interfac.c, clustalw.h
• phylogenetic_tree() : trees.cpp, trees.c, clustalw.h
• phylogenetic_tree_menu() : amenu.cpp, amenu.c
• position_scrollbars() : xmenu.h
• pred_coils() : ncoils.cpp, ncoils.h, ncoils.c, main.h
• prfalign() : prfalign.cpp, prfalign.c, clustalw.h
• prfscore() : prfalign.cpp, prfalign.c
• print_nexus_tree() : trees.cpp, trees.c
• print_phylip_tree() : trees.cpp, trees.c
• print_sec_struct_mask() : interfac.cpp, interfac.c, clustalw.h
• print_tree() : trees.cpp, trees.c
• profile_align() : interfac.cpp, interfac.c, clustalw.h
• profile_align_menu() : amenu.cpp, amenu.c
• profile_input() : interfac.cpp, interfac.c, clustalw.h
• prompt_for_yes_no() : clustalw.h, amenu.cpp, amenu.c
• prot_distance_matrix() : trees.cpp, trees.c, clustalw.h
• ptracepath() : prfalign.cpp, prfalign.c
• put_frag() : showpair.cpp, showpair.c

- r -

• read_matrix() : ncoils.cpp, read_matrix.c, ncoils.h, main.h, amenu.cpp, amenu.c
• read_matrix_series() : readmat.cpp, readmat.c, clustalw.h
• read_tree() : clustalw.h, calctree.cpp, calctree.c
• read_user_matrix() : readmat.cpp, readmat.c, clustalw.h
• readEMBL() : ureadseq.c
• readFitch() : ureadseq.c
• readGenBank() : ureadseq.c
• readIG() : ureadseq.c
• readline() : ureadseq.c
• readLoop() : ureadseq.c
• readMSF() : ureadseq.c
• readNBRF() : ureadseq.c
• readOlsen() : ureadseq.c
• readPAUPinterleaved() : ureadseq.c
• readPAUPsequential() : ureadseq.c
• readPearson() : ureadseq.c
• readPhylipInterleaved() : ureadseq.c
• readPhylipSequential() : ureadseq.c
• readPIR() : ureadseq.c
• readPlain() : ureadseq.c
• readSeq() : ureadseq.h, ureadseq.c
• readSeqFp() : ureadseq.h, ureadseq.c
• readSeqMain() : ureadseq.c
• readseqs() : sequence.cpp, sequence.c, clustalw.h
• readStrider() : ureadseq.c
• readUWGCG() : ureadseq.c
• readZuker() : ureadseq.c
• realloc_aln() : util.cpp, util.c, clustalw.h
• realloc_seq() : util.cpp, util.c, clustalw.h
• reload_alignment() : xmenu.h
• remove_gap_pos() : xmenu.h
• reroot() : calctree.cpp, calctree.c
• res_index() : sequence.cpp, sequence.c
• reset_align() : interfac.cpp, interfac.c
• reset_prf1() : interfac.cpp, interfac.c
• reset_prf2() : interfac.cpp, interfac.c
• resize_multi_window() : xmenu.h
• resize_prf_window() : xmenu.h
• ResizeWindowProc() : xmenu.h
• reverse_pass() : palign.cpp, palign.c
• rtrim() : util.cpp, util.c, clustalw.h

- s -

• save_set() : calctree.cpp, calctree.c
• secstroutput_options() : amenu.cpp, amenu.c
• select_panel() : xmenu.h
• seq_input() : interfac.cpp, interfac.c, clustalw.h
• seqalign() : malign.cpp, malign.c, clustalw.h
• seqFileFormat() : ureadseq.h, ureadseq.c
• seqFileFormatFp() : ureadseq.h, ureadseq.c
• SeqGCGCheckSum() : gcgcheck.cpp, gcgcheck.c, clustalw.h
• set_align_endgappenalties() : xmenu.h
• set_aln_mode() : xmenu.h
• set_ambiguities() : xmenu.h
• set_blocklen() : xmenu.h
• set_boot_format() : xmenu.h
• set_button() : xmenu.h
• set_case() : xmenu.h
• set_curve() : xmenu.h
• set_div_seq() : xmenu.h
• set_dnamatrix() : xmenu.h
• set_endgaps() : xmenu.h
• set_font_size() : xmenu.h
• set_format() : xmenu.h
• set_fpres() : xmenu.h
• set_fres() : xmenu.h
• set_fs_toggle() : xmenu.h
• set_gap_dist() : xmenu.h
• set_ge_penalty() : xmenu.h
• set_go_penalty() : xmenu.h
• set_gp() : xmenu.h
• set_gp_output() : xmenu.h
• set_header() : xmenu.h
• set_helix_gp() : xmenu.h
• set_helix_minus() : xmenu.h
• set_helix_plus() : xmenu.h
• set_hyd_penalties() : xmenu.h
• set_hyd_res() : xmenu.h
• set_info() : calctree.cpp, calctree.c
• set_inverted() : xmenu.h
• set_kimura() : xmenu.h
• set_ktuple() : xmenu.h
• set_lengthcutoff() : xmenu.h
• set_loop_gp() : xmenu.h
• set_lpres() : xmenu.h
• set_lres() : xmenu.h
• set_matrix() : xmenu.h
• set_neg_matrix() : xmenu.h
• set_ntrials() : xmenu.h
• set_optional_param() : interfac.cpp, interfac.c
• set_orientation() : xmenu.h
• set_output_clustal() : xmenu.h
• set_output_fasta() : xmenu.h
• set_output_gcg() : xmenu.h
• set_output_gde() : xmenu.h
• set_output_nbrf() : xmenu.h
• set_output_nexus() : xmenu.h
• set_output_order() : xmenu.h
• set_output_phylip() : xmenu.h
• set_output_pim() : xmenu.h
• set_output_tree_clustal() : xmenu.h
• set_output_tree_distances() : xmenu.h
• set_output_tree_nexus() : xmenu.h
• set_output_tree_phylip() : xmenu.h
• set_pagesize() : xmenu.h
• set_pref_penalties() : xmenu.h
• set_pscroll_mode() : xmenu.h
• set_pw_dnamatrix() : xmenu.h
• set_pw_ge_penalty() : xmenu.h
• set_pw_go_penalty() : xmenu.h
• set_pw_matrix() : xmenu.h
• set_pw_user_dnamatrix() : xmenu.h
• set_pw_user_matrix() : xmenu.h
• set_ran_seed() : xmenu.h
• set_realign_endgappenalties() : xmenu.h
• set_residue_exceptions() : xmenu.h
• set_resize() : xmenu.h
• set_resno() : xmenu.h
• set_ruler() : xmenu.h
• set_save_log() : xmenu.h
• set_save_paras() : xmenu.h
• set_score_dnamatrix() : xmenu.h
• set_score_matrix() : xmenu.h
• set_score_user_dnamatrix() : xmenu.h
• set_score_user_matrix() : xmenu.h
• set_scorecutoff() : xmenu.h
• set_scorescale() : xmenu.h
• set_segment_dnamatrix() : xmenu.h
• set_segment_dnascale() : xmenu.h
• set_segment_exceptions() : xmenu.h
• set_segment_matrix() : xmenu.h
• set_segment_user_dnamatrix() : xmenu.h
• set_segment_user_matrix() : xmenu.h
• set_show_segments() : xmenu.h
• set_snos() : xmenu.h
• set_ss_output() : xmenu.h
• set_strand_gp() : xmenu.h
• set_strand_minus() : xmenu.h
• set_strand_plus() : xmenu.h
• set_terminal_gp() : xmenu.h
• set_toggle() : xmenu.h
• set_topdiags() : xmenu.h
• set_tossgaps() : xmenu.h
• set_transitions() : xmenu.h
• set_use_ss1() : xmenu.h
• set_use_ss2() : xmenu.h
• set_user_dnamatrix() : xmenu.h
• set_user_matrix() : xmenu.h
• set_var_penalties() : xmenu.h
• set_window() : xmenu.h
• setRange() : xmenu.h
• shift() : xmenu.h
• show_aln() : interfac.cpp, interfac.c
• show_pair() : showpair.cpp, showpair.c, clustalw.h
• show_segment_exceptions() : xmenu.h
• skip_space() : calctree.cpp, calctree.c
• sort_scores() : xmenu.h
• sqlite3_aggregate_context() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_aggregate_count() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_bind_blob() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_bind_double() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_bind_int() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_bind_int64() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_bind_null() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_bind_parameter_count() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_bind_parameter_index() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_bind_parameter_name() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_bind_text() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_bind_text16() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_bind_value() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_busy_handler() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_busy_timeout() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_changes() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_clear_bindings() : mac_sqlite3.h, lin_sqlite3.h
• sqlite3_close() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_collation_needed() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_collation_needed16() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_column_blob() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_column_bytes() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_column_bytes16() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_column_count() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_column_decltype() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_column_decltype16() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_column_double() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_column_int() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_column_int64() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_column_name() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_column_name16() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_column_text() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_column_text16() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_column_type() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_commit_hook() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_complete() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_complete16() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_create_collation() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_create_collation16() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_create_function() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_create_function16() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_data_count() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_db_handle() : mac_sqlite3.h
• sqlite3_errcode() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_errmsg() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_errmsg16() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_exec() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_expired() : mac_sqlite3.h, lin_sqlite3.h
• sqlite3_finalize() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_free() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_free_table() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_get_autocommit() : mac_sqlite3.h
• sqlite3_get_auxdata() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_get_table() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_global_recover() : mac_sqlite3.h, lin_sqlite3.h
• sqlite3_interrupt() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_key() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_last_insert_rowid() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_libversion() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_libversion_number() : mac_sqlite3.h, lin_sqlite3.h
• sqlite3_mprintf() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_open() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_open16() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_prepare() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_prepare16() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_progress_handler() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_rekey() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_reset() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_result_blob() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_result_double() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_result_error() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_result_error16() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_result_int() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_result_int64() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_result_null() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_result_text() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_result_text16() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_result_text16be() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_result_text16le() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_result_value() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_set_authorizer() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_set_auxdata() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_sleep() : mac_sqlite3.h, lin_sqlite3.h
• sqlite3_snprintf() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_step() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_total_changes() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_trace() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_transfer_bindings() : mac_sqlite3.h
• sqlite3_user_data() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_value_blob() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_value_bytes() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_value_bytes16() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_value_double() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_value_int() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_value_int64() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_value_text() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_value_text16() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_value_text16be() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_value_text16le() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_value_type() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_vmprintf() : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite_aggregate_context() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_aggregate_count() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_bind() : win_sqlite.h, mac_sqlite2.h
• sqlite_busy_handler() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_busy_timeout() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_changes() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_close() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_commit_hook() : win_sqlite.h, mac_sqlite2.h
• sqlite_compile() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_complete() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_create_aggregate() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_create_function() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_decode_binary() : mac_sqlite2.h
• sqlite_encode_binary() : mac_sqlite2.h
• sqlite_error_string() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_exec() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_exec_printf() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_exec_vprintf() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_finalize() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_free_table() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_freemem() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_function_type() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_get_table() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_get_table_printf() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_get_table_vprintf() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_interrupt() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_last_insert_rowid() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_last_statement_changes() : win_sqlite.h, mac_sqlite2.h
• sqlite_libencoding() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_libversion() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_mprintf() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_open() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_open_encrypted() : win_sqlite.h, mac_sqlite2.h
• sqlite_progress_handler() : win_sqlite.h, mac_sqlite2.h
• sqlite_rekey() : win_sqlite.h, mac_sqlite2.h
• sqlite_reset() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_set_authorizer() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_set_result_double() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_set_result_error() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_set_result_int() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_set_result_string() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_step() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_trace() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_user_data() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_vmprintf() : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• ss_options_menu() : amenu.cpp, amenu.c
• startFind() : interfac.cpp, interfac.c
• Strcasecmp() : ureadseq.h, ureadseq.c
• stripspace() : xmenu.h
• Strncasecmp() : ureadseq.h, ureadseq.c
• swap() : xmenu.h
• switch_mode() : xmenu.h

- t -

• text_colors() : xmenu.h
• tracepath() : palign.cpp, palign.c
• transition() : trees.cpp, trees.c
• tree_format_options_menu() : amenu.cpp, amenu.c
• tree_gap_delete() : trees.cpp, trees.c
• two_way_split() : trees.cpp, trees.c
• two_way_split_nexus() : trees.cpp, trees.c
• txt() : main.h, main.cpp

- u -

• ungetline() : ureadseq.c
• upstr() : util.cpp, util.c, clustalw.h
• user_mat() : interfac.cpp, interfac.c, clustalw.h
• user_mat_series() : interfac.cpp, interfac.c, clustalw.h

- w -

• warning() : clustalw.h, amenu.cpp, amenu.c
• white_on_black() : xmenu.h
• write_ps_file() : xmenu.h
• writeSeq() : ureadseq.h, ureadseq.c
• WX_DECLARE_OBJARRAY() : main.h
• WX_DECLARE_STRING_HASH_MAP() : main.h, FindSequenceDialog.h
• WX_DEFINE_ARRAY() : TUndo.h, main.h
• WX_DEFINE_OBJARRAY() : main.cpp
• wxStringInsert() : main.h, main.cpp

- x -

• x_menu() : xmenu.h
• XmlTest() : xmltest.cpp

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