root/branches/stable_5.0/ARBDB/ad_t_prot.h

Revision 6077, 12.9 KB (checked in by westram, 3 years ago)
  • fix #186 + #34
    • added GBT_create_sequence_data (as replacement for GBT_add_data). Sets protection level of created 'species/ali_xxx/element' to passed value
    • added GB_copy_with_protection (after release GB_copy should generally behave like that)
    • pass write-protection selected in import-window to awtc_read_data (and removed hard-coded protection 4)
    • MG_simple_merge uses GB_copy_with_protection to copy imported species into main DB
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
Line 
1/*
2 * ARB toolkit.
3 *
4 * This file is generated by aisc_mkpt.
5 * Any changes you make here will be overwritten later!
6 *
7 */
8
9#ifndef AD_T_PROT_H
10#define AD_T_PROT_H
11
12#ifndef P_
13# error P_ is not defined
14#endif
15
16/* define ARB attributes: */
17#ifndef ATTRIBUTES_H
18# include <attributes.h>
19#endif
20
21#ifdef __cplusplus
22extern "C" {
23#endif
24
25
26/* adtools.c */
27GBDATA *GBT_find_or_create P_((GBDATA *Main, const char *key, long delete_level));
28char *GBT_get_default_helix P_((GBDATA *gb_main));
29char *GBT_get_default_helix_nr P_((GBDATA *gb_main));
30char *GBT_get_default_ref P_((GBDATA *gb_main));
31GB_ERROR GBT_check_arb_file P_((const char *name));
32char **GBT_scan_db P_((GBDATA *gbd, const char *datapath));
33void GBT_install_message_handler P_((GBDATA *gb_main));
34void GBT_message P_((GBDATA *gb_main, const char *msg));
35char **GBT_split_string P_((const char *namelist, char separator, int *countPtr));
36char *GBT_join_names P_((const char *const *names, char separator));
37void GBT_free_names P_((char **names));
38char *GBT_read_string P_((GBDATA *gb_container, const char *fieldpath));
39char *GBT_read_as_string P_((GBDATA *gb_container, const char *fieldpath));
40const char *GBT_read_char_pntr P_((GBDATA *gb_container, const char *fieldpath));
41NOT4PERL long *GBT_read_int P_((GBDATA *gb_container, const char *fieldpath));
42NOT4PERL double *GBT_read_float P_((GBDATA *gb_container, const char *fieldpath));
43char *GBT_readOrCreate_string P_((GBDATA *gb_container, const char *fieldpath, const char *default_value));
44const char *GBT_readOrCreate_char_pntr P_((GBDATA *gb_container, const char *fieldpath, const char *default_value));
45NOT4PERL long *GBT_readOrCreate_int P_((GBDATA *gb_container, const char *fieldpath, long default_value));
46NOT4PERL double *GBT_readOrCreate_float P_((GBDATA *gb_container, const char *fieldpath, double default_value));
47GB_ERROR GBT_write_string P_((GBDATA *gb_container, const char *fieldpath, const char *content));
48GB_ERROR GBT_write_int P_((GBDATA *gb_container, const char *fieldpath, long content));
49GB_ERROR GBT_write_byte P_((GBDATA *gb_container, const char *fieldpath, unsigned char content));
50GB_ERROR GBT_write_float P_((GBDATA *gb_container, const char *fieldpath, double content));
51GBDATA *GB_test_link_follower P_((GBDATA *gb_main, GBDATA *gb_link, const char *link));
52GBDATA *GBT_open P_((const char *path, const char *opent, const char *disabled_path));
53GB_ERROR GBT_remote_action P_((GBDATA *gb_main, const char *application, const char *action_name));
54GB_ERROR GBT_remote_awar P_((GBDATA *gb_main, const char *application, const char *awar_name, const char *value));
55GB_ERROR GBT_remote_read_awar P_((GBDATA *gb_main, const char *application, const char *awar_name));
56const char *GBT_remote_touch_awar P_((GBDATA *gb_main, const char *application, const char *awar_name));
57char *GB_generate_notification P_((GBDATA *gb_main, void (*cb )(const char *message, void *client_data ), const char *message, void *client_data));
58GB_ERROR GB_remove_last_notification P_((GBDATA *gb_main));
59GB_ERROR GB_notify P_((GBDATA *gb_main, int id, const char *message));
60
61/* adseqcompr.c */
62GB_ERROR GBT_compress_sequence_tree2 P_((GBDATA *gb_main, const char *tree_name, const char *ali_name));
63void GBT_compression_test P_((void *dummy, GBDATA *gb_main));
64
65/* adtables.c */
66GB_ERROR GBT_install_table_link_follower P_((GBDATA *gb_main));
67GBDATA *GBT_open_table P_((GBDATA *gb_table_root, const char *table_name, GB_BOOL read_only));
68GBDATA *GBT_first_table P_((GBDATA *gb_main));
69GBDATA *GBT_next_table P_((GBDATA *gb_table));
70GBDATA *GBT_first_table_entry P_((GBDATA *gb_table));
71GBDATA *GBT_first_marked_table_entry P_((GBDATA *gb_table));
72GBDATA *GBT_next_table_entry P_((GBDATA *gb_table_entry));
73GBDATA *GBT_next_marked_table_entry P_((GBDATA *gb_table_entry));
74GBDATA *GBT_find_table_entry P_((GBDATA *gb_table, const char *id));
75GBDATA *GBT_open_table_entry P_((GBDATA *gb_table, const char *id));
76GBDATA *GBT_first_table_field P_((GBDATA *gb_table));
77GBDATA *GBT_first_marked_table_field P_((GBDATA *gb_table));
78GBDATA *GBT_next_table_field P_((GBDATA *gb_table_field));
79GBDATA *GBT_next_marked_table_field P_((GBDATA *gb_table_field));
80GBDATA *GBT_find_table_field P_((GBDATA *gb_table, const char *id));
81GB_TYPES GBT_get_type_of_table_entry_field P_((GBDATA *gb_table, const char *fieldname));
82GB_ERROR GBT_savely_write_table_entry_field P_((GBDATA *gb_table, GBDATA *gb_entry, const char *fieldname, const char *value_in_ascii_format));
83GBDATA *GBT_open_table_field P_((GBDATA *gb_table, const char *fieldname, GB_TYPES type_of_field));
84
85/* adRevCompl.c */
86char GBT_complementNucleotide P_((char c, char T_or_U));
87char *GBT_reverseNucSequence P_((const char *s, int len));
88char *GBT_complementNucSequence P_((const char *s, int len, char T_or_U));
89GB_ERROR GBT_determine_T_or_U P_((GB_alignment_type alignment_type, char *T_or_U, const char *supposed_target));
90void GBT_reverseComplementNucSequence P_((char *seq, long length, char T_or_U));
91
92/* adChangeKey.c */
93GBDATA *GBT_get_changekey P_((GBDATA *gb_main, const char *key, const char *change_key_path));
94GB_TYPES GBT_get_type_of_changekey P_((GBDATA *gb_main, const char *field_name, const char *change_key_path));
95GB_ERROR GBT_add_new_changekey_to_keypath P_((GBDATA *gb_main, const char *name, int type, const char *keypath));
96GB_ERROR GBT_add_new_changekey P_((GBDATA *gb_main, const char *name, int type));
97GB_ERROR GBT_add_new_gene_changekey P_((GBDATA *gb_main, const char *name, int type));
98GB_ERROR GBT_add_new_experiment_changekey P_((GBDATA *gb_main, const char *name, int type));
99GB_ERROR GBT_convert_changekey P_((GBDATA *gb_main, const char *name, int target_type));
100
101/* adali.c */
102GB_ERROR GBT_check_data P_((GBDATA *Main, const char *alignment_name));
103char **GBT_get_alignment_names P_((GBDATA *gbd));
104GB_ERROR GBT_check_alignment_name P_((const char *alignment_name));
105GBDATA *GBT_create_alignment P_((GBDATA *gbd, const char *name, long len, long aligned, long security, const char *type));
106NOT4PERL GB_ERROR GBT_check_alignment P_((GBDATA *gb_main, GBDATA *preset_alignment, GB_HASH *species_name_hash));
107GB_ERROR GBT_rename_alignment P_((GBDATA *gbMain, const char *source, const char *dest, int copy, int dele));
108GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED;
109NOT4PERL GBDATA *GBT_create_sequence_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type, int security_write));
110GB_ERROR GBT_write_sequence P_((GBDATA *gb_data, const char *ali_name, long ali_len, const char *sequence));
111GBDATA *GBT_gen_accession_number P_((GBDATA *gb_species, const char *ali_name));
112int GBT_is_partial P_((GBDATA *gb_species, int default_value, int define_if_undef));
113GBDATA *GBT_read_sequence P_((GBDATA *gb_species, const char *aliname));
114char *GBT_get_default_alignment P_((GBDATA *gb_main));
115GB_ERROR GBT_set_default_alignment P_((GBDATA *gb_main, const char *alignment_name));
116GBDATA *GBT_get_alignment P_((GBDATA *gb_main, const char *aliname));
117long GBT_get_alignment_len P_((GBDATA *gb_main, const char *aliname));
118GB_ERROR GBT_set_alignment_len P_((GBDATA *gb_main, const char *aliname, long new_len));
119int GBT_get_alignment_aligned P_((GBDATA *gb_main, const char *aliname));
120char *GBT_get_alignment_type_string P_((GBDATA *gb_main, const char *aliname));
121GB_alignment_type GBT_get_alignment_type P_((GBDATA *gb_main, const char *aliname));
122GB_BOOL GBT_is_alignment_protein P_((GBDATA *gb_main, const char *alignment_name));
123NOT4PERL char *GBT_read_gene_sequence_and_length P_((GBDATA *gb_gene, GB_BOOL use_revComplement, char partSeparator, size_t *gene_length));
124char *GBT_read_gene_sequence P_((GBDATA *gb_gene, GB_BOOL use_revComplement, char partSeparator));
125
126/* adcolumns.c */
127GB_ERROR GBT_format_alignment P_((GBDATA *Main, const char *alignment_name));
128GB_ERROR GBT_insert_character P_((GBDATA *Main, char *alignment_name, long pos, long count, char *char_delete));
129
130/* adtree.c */
131GBT_TREE *GBT_remove_leafs P_((GBT_TREE *tree, GBT_TREE_REMOVE_TYPE mode, GB_HASH *species_hash, int *removed, int *groups_removed));
132void GBT_delete_tree P_((GBT_TREE *tree));
133GB_ERROR GBT_write_group_name P_((GBDATA *gb_group_name, const char *new_group_name));
134GB_ERROR GBT_write_tree P_((GBDATA *gb_main, GBDATA *gb_tree, const char *tree_name, GBT_TREE *tree));
135GB_ERROR GBT_write_plain_tree P_((GBDATA *gb_main, GBDATA *gb_tree, char *tree_name, GBT_TREE *tree));
136GB_ERROR GBT_write_tree_rem P_((GBDATA *gb_main, const char *tree_name, const char *remark));
137GBT_TREE *GBT_read_tree_and_size P_((GBDATA *gb_main, const char *tree_name, long structure_size, int *tree_size));
138GBT_TREE *GBT_read_tree P_((GBDATA *gb_main, const char *tree_name, long structure_size));
139GBT_TREE *GBT_read_plain_tree P_((GBDATA *gb_main, GBDATA *gb_ctree, long structure_size, GB_ERROR *error));
140long GBT_count_nodes P_((GBT_TREE *tree));
141GB_ERROR GBT_link_tree_using_species_hash P_((GBT_TREE *tree, GB_BOOL show_status, GB_HASH *species_hash, int *zombies, int *duplicates));
142GB_ERROR GBT_link_tree P_((GBT_TREE *tree, GBDATA *gb_main, GB_BOOL show_status, int *zombies, int *duplicates));
143void GBT_unlink_tree P_((GBT_TREE *tree));
144GBDATA *GBT_get_tree P_((GBDATA *gb_main, const char *tree_name));
145long GBT_size_of_tree P_((GBDATA *gb_main, const char *tree_name));
146char *GBT_find_largest_tree P_((GBDATA *gb_main));
147char *GBT_find_latest_tree P_((GBDATA *gb_main));
148const char *GBT_tree_info_string P_((GBDATA *gb_main, const char *tree_name, int maxTreeNameLen));
149GB_ERROR GBT_check_tree_name P_((const char *tree_name));
150char **GBT_get_tree_names_and_count P_((GBDATA *Main, int *countPtr));
151char **GBT_get_tree_names P_((GBDATA *Main));
152char *GBT_get_next_tree_name P_((GBDATA *gb_main, const char *tree_name));
153GB_CSTR *GBT_get_species_names_of_tree P_((GBT_TREE *tree));
154char *GBT_existing_tree P_((GBDATA *gb_main, const char *tree_name));
155
156/* adname.c */
157GB_ERROR GBT_begin_rename_session P_((GBDATA *gb_main, int all_flag));
158GB_ERROR GBT_rename_species P_((const char *oldname, const char *newname, GB_BOOL ignore_protection));
159GB_ERROR GBT_abort_rename_session P_((void));
160GB_ERROR GBT_commit_rename_session P_((int (*show_status )(double gauge ), int (*show_status_text )(const char *)));
161
162/* aditem.c */
163GBDATA *GBT_find_or_create_item_rel_item_data P_((GBDATA *gb_item_data, const char *itemname, const char *id_field, const char *id, GB_BOOL markCreated));
164GBDATA *GBT_find_or_create_species_rel_species_data P_((GBDATA *gb_species_data, const char *name));
165GBDATA *GBT_find_or_create_species P_((GBDATA *gb_main, const char *name));
166GBDATA *GBT_find_or_create_SAI P_((GBDATA *gb_main, const char *name));
167GBDATA *GBT_find_item_rel_item_data P_((GBDATA *gb_item_data, const char *id_field, const char *id_value));
168GBDATA *GBT_expect_item_rel_item_data P_((GBDATA *gb_item_data, const char *id_field, const char *id_value));
169GBDATA *GBT_get_species_data P_((GBDATA *gb_main));
170GBDATA *GBT_first_marked_species_rel_species_data P_((GBDATA *gb_species_data));
171GBDATA *GBT_first_marked_species P_((GBDATA *gb_main));
172GBDATA *GBT_next_marked_species P_((GBDATA *gb_species));
173GBDATA *GBT_first_species_rel_species_data P_((GBDATA *gb_species_data));
174GBDATA *GBT_first_species P_((GBDATA *gb_main));
175GBDATA *GBT_next_species P_((GBDATA *gb_species));
176GBDATA *GBT_find_species_rel_species_data P_((GBDATA *gb_species_data, const char *name));
177GBDATA *GBT_find_species P_((GBDATA *gb_main, const char *name));
178GBDATA *GBT_expect_species P_((GBDATA *gb_main, const char *name));
179GBDATA *GBT_get_SAI_data P_((GBDATA *gb_main));
180GBDATA *GBT_first_marked_SAI_rel_SAI_data P_((GBDATA *gb_sai_data));
181GBDATA *GBT_next_marked_SAI P_((GBDATA *gb_sai));
182GBDATA *GBT_first_SAI_rel_SAI_data P_((GBDATA *gb_sai_data));
183GBDATA *GBT_first_SAI P_((GBDATA *gb_main));
184GBDATA *GBT_next_SAI P_((GBDATA *gb_sai));
185GBDATA *GBT_find_SAI_rel_SAI_data P_((GBDATA *gb_sai_data, const char *name));
186GBDATA *GBT_find_SAI P_((GBDATA *gb_main, const char *name));
187GBDATA *GBT_expect_SAI P_((GBDATA *gb_main, const char *name));
188long GBT_get_item_count P_((GBDATA *gb_parent_of_container, const char *item_container_name));
189long GBT_get_species_count P_((GBDATA *gb_main));
190long GBT_get_SAI_count P_((GBDATA *gb_main));
191char *GBT_create_unique_item_identifier P_((GBDATA *gb_item_container, const char *id_field, const char *default_id));
192char *GBT_create_unique_species_name P_((GBDATA *gb_main, const char *default_name));
193void GBT_mark_all P_((GBDATA *gb_main, int flag));
194void GBT_mark_all_that P_((GBDATA *gb_main, int flag, int (*condition )(GBDATA *, void *), void *cd));
195long GBT_count_marked_species P_((GBDATA *gb_main));
196char *GBT_store_marked_species P_((GBDATA *gb_main, int unmark_all));
197NOT4PERL GB_ERROR GBT_with_stored_species P_((GBDATA *gb_main, const char *stored, species_callback doit, int *clientdata));
198GB_ERROR GBT_restore_marked_species P_((GBDATA *gb_main, const char *stored_marked));
199GB_CSTR GBT_read_name P_((GBDATA *gb_item));
200const char *GBT_get_name P_((GBDATA *gb_item));
201GBDATA **GBT_gen_species_array P_((GBDATA *gb_main, long *pspeccnt));
202
203#ifdef __cplusplus
204}
205#endif
206
207#else
208#error ad_t_prot.h included twice
209#endif /* AD_T_PROT_H */
Note: See TracBrowser for help on using the browser.