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source: tags/initial/ARBDB/ad_t_prot.h

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Last change on this file was 2, checked in by oldcode, 23 years ago
Initial revision
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 8.4 KB

Line
1	#ifndef P_
2	# error P_ is not defined
3	#endif
4
5	#ifdef __cplusplus
6	extern "C" {
7	#endif
8
9	/* adtools.c */
10	char *GBT_get_alignment_names P_((GBDATA gbd));
11	GB_ERROR GBT_check_alignment_name P_((const char *alignment_name));
12	GBDATA GBT_create_alignment P_((GBDATA gbd, const char name, long len, long aligned, long security, const char type));
13	GB_ERROR GBT_check_alignment P_((GBDATA Main, GBDATA preset_alignment));
14	GB_ERROR GBT_rename_alignment P_((GBDATA gbd, const char source, const char *dest, int copy, int dele));
15	GBDATA GBT_find_or_create P_((GBDATA Main, const char *key, long delete_level));
16	GB_ERROR GBT_check_data P_((GBDATA Main, char alignment_name));
17	GB_ERROR GBT_check_lengths P_((GBDATA Main, const char alignment_name));
18	GB_ERROR GBT_insert_character P_((GBDATA Main, char alignment_name, long pos, long count, char *char_delete));
19	GB_ERROR GBT_delete_tree P_((GBT_TREE *tree));
20	GB_ERROR GBT_write_tree P_((GBDATA gb_main, GBDATA gb_tree, char tree_name, GBT_TREE tree));
21	GB_ERROR GBT_write_tree_rem P_((GBDATA gb_main, const char tree_name, const char *remark));
22	GBT_TREE GBT_read_tree_and_size P_((GBDATA gb_main, const char tree_name, long structure_size, int tree_size));
23	GBT_TREE GBT_read_tree P_((GBDATA gb_main, const char *tree_name, long structure_size));
24	GB_ERROR GBT_link_tree P_((GBT_TREE tree, GBDATA gb_main, GB_BOOL show_status));
25	GBT_TREE GBT_load_tree P_((char path, int structuresize));
26	GBDATA GBT_get_tree P_((GBDATA gb_main, const char *tree_name));
27	long GBT_size_of_tree P_((GBDATA gb_main, const char tree_name));
28	char GBT_find_largest_tree P_((GBDATA gb_main));
29	char GBT_find_latest_tree P_((GBDATA gb_main));
30	char GBT_tree_info_string P_((GBDATA gb_main, const char *tree_name));
31	GB_ERROR GBT_check_tree_name P_((const char *tree_name));
32	char *GBT_get_tree_names P_((GBDATA Main));
33	char GBT_get_next_tree_name P_((GBDATA gb_main, const char *tree));
34	GB_ERROR GBT_free_names P_((char **names));
35	GB_CSTR GBT_get_species_names_of_tree P_((GBT_TREE tree));
36	char GBT_existing_tree P_((GBDATA Main, const char *tree));
37	GB_ERROR GBT_export_tree P_((GBDATA gb_main, FILE out, GBT_TREE *tree, GB_BOOL triple_root));
38	GBDATA GBT_create_species P_((GBDATA gb_main, const char *name));
39	GBDATA GBT_create_species_rel_species_data P_((GBDATA gb_species_data, const char *name));
40	GBDATA GBT_create_SAI P_((GBDATA gb_main, const char *name));
41	GBDATA GBT_add_data P_((GBDATA species, const char ali_name, const char key, GB_TYPES type));
42	GB_ERROR GBT_write_sequence P_((GBDATA gb_data, const char ali_name, long ali_len, const char *sequence));
43	GBDATA GBT_gen_accession_number P_((GBDATA gb_species, const char *ali_name));
44	GBDATA GBT_first_marked_species_rel_species_data P_((GBDATA gb_species_data));
45	GBDATA GBT_first_marked_species P_((GBDATA gb_main));
46	GBDATA GBT_next_marked_species P_((GBDATA gb_species));
47	GBDATA GBT_first_species_rel_species_data P_((GBDATA gb_species_data));
48	GBDATA GBT_first_species P_((GBDATA gb_main));
49	GBDATA GBT_next_species P_((GBDATA gb_species));
50	GBDATA GBT_find_species_rel_species_data P_((GBDATA gb_species_data, const char *name));
51	GBDATA GBT_find_species P_((GBDATA gb_main, const char *name));
52	GBDATA GBT_first_marked_extended P_((GBDATA gb_extended_data));
53	GBDATA GBT_next_marked_extended P_((GBDATA gb_extended));
54	GBDATA GBT_first_SAI P_((GBDATA gb_main));
55	GBDATA GBT_next_SAI P_((GBDATA gb_extended));
56	GBDATA GBT_find_SAI P_((GBDATA gb_main, const char *name));
57	GBDATA GBT_first_SAI_rel_exdata P_((GBDATA gb_extended_data));
58	GBDATA GBT_find_SAI_rel_exdata P_((GBDATA gb_extended_data, const char *name));
59	char GBT_create_unique_species_name P_((GBDATA gb_main, const char *default_name));
60	GBDATA GBT_find_configuration P_((GBDATA gb_main, const char *name));
61	GBDATA GBT_create_configuration P_((GBDATA gb_main, const char *name));
62	void GBT_mark_all P_((GBDATA *gb_main, int flag));
63	long GBT_count_marked_species P_((GBDATA *gb_main));
64	long GBT_count_species P_((GBDATA *gb_main));
65	long GBT_recount_species P_((GBDATA *gb_main));
66	GBDATA GBT_read_sequence P_((GBDATA gb_species, const char *use));
67	char GBT_read_name P_((GBDATA gb_species));
68	char GBT_get_default_alignment P_((GBDATA gb_main));
69	GB_ERROR GBT_set_default_alignment P_((GBDATA gb_main, const char alignment_name));
70	char GBT_get_default_helix P_((GBDATA gb_main));
71	char GBT_get_default_helix_nr P_((GBDATA gb_main));
72	char GBT_get_default_ref P_((GBDATA gb_main));
73	GBDATA GBT_get_alignment P_((GBDATA gb_main, const char *use));
74	long GBT_get_alignment_len P_((GBDATA gb_main, const char use));
75	GB_ERROR GBT_set_alignment_len P_((GBDATA gb_main, const char use, long new_len));
76	int GBT_get_alignment_aligned P_((GBDATA gb_main, const char use));
77	char GBT_get_alignment_type_string P_((GBDATA gb_main, const char *use));
78	GB_alignment_type GBT_get_alignment_type P_((GBDATA gb_main, const char use));
79	GB_BOOL GBT_is_alignment_protein P_((GBDATA gb_main, const char alignment_name));
80	GB_ERROR GBT_check_arb_file P_((const char *name));
81	char *GBT_scan_db P_((GBDATA gbd));
82	GB_ERROR GBT_message P_((GBDATA gb_main, const char msg));
83	GB_HASH GBT_generate_species_hash P_((GBDATA gb_main, int ncase));
84	GB_HASH GBT_generate_marked_species_hash P_((GBDATA gb_main));
85	GB_ERROR GBT_begin_rename_session P_((GBDATA *gb_main, int all_flag));
86	GB_ERROR GBT_rename_species P_((const char oldname, const char newname));
87	GB_ERROR GBT_abort_rename_session P_((void));
88	GB_ERROR GBT_commit_rename_session P_((int (*show_status )(double gauge )));
89	GBDATA *GBT_gen_species_array P_((GBDATA gb_main, long *pspeccnt));
90	char GBT_read_string P_((GBDATA gb_main, const char *awar_name));
91	long GBT_read_int P_((GBDATA gb_main, const char awar_name));
92	double GBT_read_float P_((GBDATA gb_main, const char awar_name));
93	GBDATA GBT_search_string P_((GBDATA gb_main, const char awar_name, const char def));
94	GBDATA GBT_search_int P_((GBDATA gb_main, const char *awar_name, int def));
95	GBDATA GBT_search_float P_((GBDATA gb_main, const char *awar_name, double def));
96	char GBT_read_string2 P_((GBDATA gb_main, const char awar_name, const char def));
97	long GBT_read_int2 P_((GBDATA gb_main, const char awar_name, long def));
98	double GBT_read_float2 P_((GBDATA gb_main, const char awar_name, double def));
99	GB_ERROR GBT_write_string P_((GBDATA gb_main, const char awar_name, const char *def));
100	GB_ERROR GBT_write_int P_((GBDATA gb_main, const char awar_name, long def));
101	GB_ERROR GBT_write_float P_((GBDATA gb_main, const char awar_name, double def));
102	GBDATA GB_test_link_follower P_((GBDATA gb_main, GBDATA gb_link, const char link));
103	GBDATA GBT_open P_((const char path, const char opent, const char disabled_path));
104	GB_ERROR GBT_remote_action P_((GBDATA gb_main, const char application, const char *action_name));
105	GB_ERROR GBT_remote_awar P_((GBDATA gb_main, const char application, const char awar_name, const char value));
106
107	/* adseqcompr.c */
108	GB_ERROR GBT_compress_sequence_tree P_((GBDATA gb_main, GB_CTREE tree, const char *ali_name));
109	GB_ERROR GBT_compress_sequence_tree2 P_((GBDATA gb_main, const char tree_name, const char *ali_name));
110	void GBT_compression_test P_((void dummy, GBDATA gb_main));
111
112	/* adtables.c */
113	GB_ERROR GBT_install_table_link_follower P_((GBDATA *gb_main));
114	GBDATA GBT_open_table P_((GBDATA gb_table_root, const char *table_name, GB_BOOL read_only));
115	GBDATA GBT_first_table P_((GBDATA gb_main));
116	GBDATA GBT_next_table P_((GBDATA gb_table));
117	GBDATA GBT_first_table_entry P_((GBDATA gb_table));
118	GBDATA GBT_first_marked_table_entry P_((GBDATA gb_table));
119	GBDATA GBT_next_table_entry P_((GBDATA gb_table_entry));
120	GBDATA GBT_next_marked_table_entry P_((GBDATA gb_table_entry));
121	GBDATA GBT_find_table_entry P_((GBDATA gb_table, const char *id));
122	GBDATA GBT_open_table_entry P_((GBDATA gb_table, const char *id));
123	GBDATA GBT_first_table_field P_((GBDATA gb_table));
124	GBDATA GBT_first_marked_table_field P_((GBDATA gb_table));
125	GBDATA GBT_next_table_field P_((GBDATA gb_table_field));
126	GBDATA GBT_next_marked_table_field P_((GBDATA gb_table_field));
127	GBDATA GBT_find_table_field P_((GBDATA gb_table, const char *id));
128	GB_TYPES GBT_get_type_of_table_entry_field P_((GBDATA gb_table, const char fieldname));
129	GB_ERROR GBT_savely_write_table_entry_field P_((GBDATA gb_table, GBDATA gb_entry, const char fieldname, const char value_in_ascii_format));
130	GBDATA GBT_open_table_field P_((GBDATA gb_table, const char *fieldname, GB_TYPES type_of_field));
131
132	#ifdef __cplusplus
133	}
134	#endif

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