1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
|
/* ARB toolkit.
*
* This file is generated by aisc_mkpt.
* Any changes you make here will be overwritten later!
*/
#ifndef AD_T_PROT_H
#define AD_T_PROT_H
/* define ARB attributes: */
#ifndef ATTRIBUTES_H
# include <attributes.h>
#endif
/* adChangeKey.cxx */
GBDATA *GBT_get_changekey(GBDATA *gb_main, const char *key, const char *change_key_path);
GB_TYPES GBT_get_type_of_changekey(GBDATA *gb_main, const char *field_name, const char *change_key_path);
GB_ERROR GBT_add_new_changekey_to_keypath(GBDATA *gb_main, const char *name, int type, const char *keypath);
GB_ERROR GBT_add_new_changekey(GBDATA *gb_main, const char *name, int type);
GB_ERROR GBT_add_new_gene_changekey(GBDATA *gb_main, const char *name, int type);
GB_ERROR GBT_add_new_experiment_changekey(GBDATA *gb_main, const char *name, int type);
GB_ERROR GBT_convert_changekey(GBDATA *gb_main, const char *name, GB_TYPES target_type);
/* adRevCompl.cxx */
char *GBT_reverseNucSequence(const char *s, int len);
char *GBT_complementNucSequence(const char *s, int len, char T_or_U);
NOT4PERL GB_ERROR GBT_determine_T_or_U(GB_alignment_type alignment_type, char *T_or_U, const char *supposed_target);
NOT4PERL void GBT_reverseComplementNucSequence(char *seq, long length, char T_or_U);
/* adali.cxx */
GBDATA *GBT_get_presets(GBDATA *gb_main);
int GBT_count_alignments(GBDATA *gb_main);
GB_ERROR GBT_check_data(GBDATA *Main, const char *alignment_name);
void GBT_get_alignment_names(ConstStrArray& names, GBDATA *gbd);
GB_ERROR GBT_check_alignment_name(const char *alignment_name);
GBDATA *GBT_create_alignment(GBDATA *gbd, const char *name, long len, long aligned, long security, const char *type);
GB_ERROR GBT_rename_alignment(GBDATA *gbMain, const char *source, const char *dest, int copy, int dele);
NOT4PERL GBDATA *GBT_add_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type) __ATTR__DEPRECATED_TODO("better use GBT_create_sequence_data()");
NOT4PERL GBDATA *GBT_create_sequence_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type, int security_write);
GB_ERROR GBT_write_sequence(GBDATA *gb_data, const char *ali_name, long ali_len, const char *sequence);
GBDATA *GBT_gen_accession_number(GBDATA *gb_species, const char *ali_name);
int GBT_is_partial(GBDATA *gb_species, int default_value, bool define_if_undef);
GBDATA *GBT_read_sequence(GBDATA *gb_species, const char *aliname);
char *GBT_get_default_alignment(GBDATA *gb_main);
GB_ERROR GBT_set_default_alignment(GBDATA *gb_main, const char *alignment_name);
GBDATA *GBT_get_alignment(GBDATA *gb_main, const char *aliname);
long GBT_get_alignment_len(GBDATA *gb_main, const char *aliname);
GB_ERROR GBT_set_alignment_len(GBDATA *gb_main, const char *aliname, long new_len);
char *GBT_get_alignment_type_string(GBDATA *gb_main, const char *aliname);
GB_alignment_type GBT_get_alignment_type(GBDATA *gb_main, const char *aliname);
bool GBT_is_alignment_protein(GBDATA *gb_main, const char *alignment_name);
NOT4PERL char *GBT_read_gene_sequence_and_length(GBDATA *gb_gene, bool use_revComplement, char partSeparator, size_t *gene_length);
char *GBT_read_gene_sequence(GBDATA *gb_gene, bool use_revComplement, char partSeparator);
/* aditem.cxx */
GBDATA *GBT_find_or_create_item_rel_item_data(GBDATA *gb_item_data, const char *itemname, const char *id_field, const char *id, bool markCreated);
GBDATA *GBT_find_or_create_species_rel_species_data(GBDATA *gb_species_data, const char *name);
GBDATA *GBT_find_or_create_species(GBDATA *gb_main, const char *name);
GBDATA *GBT_find_or_create_SAI(GBDATA *gb_main, const char *name);
GBDATA *GBT_find_item_rel_item_data(GBDATA *gb_item_data, const char *id_field, const char *id_value);
GBDATA *GBT_get_species_data(GBDATA *gb_main);
GBDATA *GBT_first_marked_species_rel_species_data(GBDATA *gb_species_data);
GBDATA *GBT_first_marked_species(GBDATA *gb_main);
GBDATA *GBT_next_marked_species(GBDATA *gb_species);
GBDATA *GBT_first_species_rel_species_data(GBDATA *gb_species_data);
GBDATA *GBT_first_species(GBDATA *gb_main);
GBDATA *GBT_next_species(GBDATA *gb_species);
GBDATA *GBT_find_species_rel_species_data(GBDATA *gb_species_data, const char *name);
GBDATA *GBT_find_species(GBDATA *gb_main, const char *name);
GBDATA *GBT_expect_species(GBDATA *gb_main, const char *name);
GBDATA *GBT_get_SAI_data(GBDATA *gb_main);
GBDATA *GBT_first_SAI_rel_SAI_data(GBDATA *gb_sai_data);
GBDATA *GBT_first_SAI(GBDATA *gb_main);
GBDATA *GBT_next_SAI(GBDATA *gb_sai);
GBDATA *GBT_find_SAI_rel_SAI_data(GBDATA *gb_sai_data, const char *name);
GBDATA *GBT_find_SAI(GBDATA *gb_main, const char *name);
GBDATA *GBT_expect_SAI(GBDATA *gb_main, const char *name);
long GBT_get_species_count(GBDATA *gb_main);
long GBT_get_SAI_count(GBDATA *gb_main);
char *GBT_create_unique_species_name(GBDATA *gb_main, const char *default_name);
void GBT_mark_all(GBDATA *gb_main, int flag);
void GBT_mark_all_that(GBDATA *gb_main, int flag, int (*condition)(GBDATA *, void *), void *cd);
long GBT_count_marked_species(GBDATA *gb_main);
char *GBT_store_marked_species(GBDATA *gb_main, int unmark_all);
NOT4PERL GB_ERROR GBT_with_stored_species(GBDATA *gb_main, const char *stored, species_callback doit, int *clientdata);
GB_ERROR GBT_restore_marked_species(GBDATA *gb_main, const char *stored_marked);
GB_CSTR GBT_read_name(GBDATA *gb_item);
const char *GBT_get_name(GBDATA *gb_item);
GBDATA **GBT_gen_species_array(GBDATA *gb_main, long *pspeccnt);
/* adname.cxx */
GB_ERROR GBT_begin_rename_session(GBDATA *gb_main, int all_flag);
GB_ERROR GBT_rename_species(const char *oldname, const char *newname, bool ignore_protection);
GB_ERROR GBT_abort_rename_session(void);
GB_ERROR GBT_commit_rename_session(void) __ATTR__USERESULT;
/* adseqcompr.cxx */
GB_ERROR GBT_compress_sequence_tree2(GBDATA *gbd, const char *tree_name, const char *ali_name) __ATTR__USERESULT;
void GBT_compression_test(void *, GBDATA *gb_main);
/* adtables.cxx */
GB_ERROR GBT_install_table_link_follower(GBDATA *gb_main);
GBDATA *GBT_open_table(GBDATA *gb_table_root, const char *table_name, bool read_only);
GBDATA *GBT_first_table(GBDATA *gb_main);
GBDATA *GBT_next_table(GBDATA *gb_table);
GBDATA *GBT_first_table_entry(GBDATA *gb_table);
GBDATA *GBT_next_table_entry(GBDATA *gb_table_entry);
GBDATA *GBT_first_table_field(GBDATA *gb_table);
GBDATA *GBT_next_table_field(GBDATA *gb_table_field);
GBDATA *GBT_find_table_field(GBDATA *gb_table, const char *id);
GBDATA *GBT_open_table_field(GBDATA *gb_table, const char *fieldname, GB_TYPES type_of_field);
/* adtools.cxx */
GBDATA *GBT_create(GBDATA *father, const char *key, long delete_level);
GBDATA *GBT_find_or_create(GBDATA *father, const char *key, long delete_level);
char *GBT_get_default_helix(GBDATA *);
char *GBT_get_default_helix_nr(GBDATA *);
char *GBT_get_default_ref(GBDATA *);
void GBT_scan_db(StrArray& fieldNames, GBDATA *gbd, const char *datapath);
void GBT_install_message_handler(GBDATA *gb_main);
void GBT_message(GBDATA *gb_main, const char *msg);
char *GBT_read_string(GBDATA *gb_container, const char *fieldpath);
char *GBT_read_as_string(GBDATA *gb_container, const char *fieldpath);
const char *GBT_read_char_pntr(GBDATA *gb_container, const char *fieldpath);
NOT4PERL long *GBT_read_int(GBDATA *gb_container, const char *fieldpath);
NOT4PERL double *GBT_read_float(GBDATA *gb_container, const char *fieldpath);
char *GBT_readOrCreate_string(GBDATA *gb_container, const char *fieldpath, const char *default_value);
const char *GBT_readOrCreate_char_pntr(GBDATA *gb_container, const char *fieldpath, const char *default_value);
NOT4PERL long *GBT_readOrCreate_int(GBDATA *gb_container, const char *fieldpath, long default_value);
NOT4PERL double *GBT_readOrCreate_float(GBDATA *gb_container, const char *fieldpath, double default_value);
GB_ERROR GBT_write_string(GBDATA *gb_container, const char *fieldpath, const char *content);
GB_ERROR GBT_write_int(GBDATA *gb_container, const char *fieldpath, long content);
GB_ERROR GBT_write_byte(GBDATA *gb_container, const char *fieldpath, unsigned char content);
GB_ERROR GBT_write_float(GBDATA *gb_container, const char *fieldpath, double content);
GBDATA *GBT_open(const char *path, const char *opent);
GB_ERROR GB_set_macro_error(GBDATA *gb_main, const char *curr_error);
GB_ERROR GB_get_macro_error(GBDATA *gb_main);
GB_ERROR GB_clear_macro_error(GBDATA *gb_main);
GB_ERROR GBT_remote_action(GBDATA *gb_main, const char *application, const char *action_name);
GB_ERROR GBT_remote_awar(GBDATA *gb_main, const char *application, const char *awar_name, const char *value);
GB_ERROR GBT_remote_read_awar(GBDATA *gb_main, const char *application, const char *awar_name);
const char *GBT_relativeMacroname(const char *macro_name);
GB_ERROR GBT_macro_execute(const char *macro_name, bool loop_marked, bool run_async);
char *GB_generate_notification(GBDATA *gb_main, void (*cb)(const char *message, void *client_data), const char *message, void *client_data);
GB_ERROR GB_remove_last_notification(GBDATA *gb_main);
GB_ERROR GB_notify(GBDATA *gb_main, int id, const char *message);
/* adtree.cxx */
GBDATA *GBT_get_tree_data(GBDATA *gb_main);
GBT_TREE *GBT_remove_leafs(GBT_TREE *tree, GBT_TreeRemoveType mode, const GB_HASH *species_hash, int *removed, int *groups_removed);
GB_ERROR GBT_write_group_name(GBDATA *gb_group_name, const char *new_group_name);
GB_ERROR GBT_write_tree(GBDATA *gb_main, const char *tree_name, GBT_TREE *tree);
GB_ERROR GBT_overwrite_tree(GBDATA *gb_tree, GBT_TREE *tree);
GB_ERROR GBT_write_tree_remark(GBDATA *gb_main, const char *tree_name, const char *remark);
GB_ERROR GBT_log_to_tree_remark(GBDATA *gb_tree, const char *log_entry);
GB_ERROR GBT_log_to_tree_remark(GBDATA *gb_main, const char *tree_name, const char *log_entry);
GB_ERROR GBT_write_tree_with_remark(GBDATA *gb_main, const char *tree_name, GBT_TREE *tree, const char *remark);
GBT_TREE *GBT_read_tree_and_size(GBDATA *gb_main, const char *tree_name, const TreeNodeFactory& nodeFactory, int *tree_size);
GBT_TREE *GBT_read_tree(GBDATA *gb_main, const char *tree_name, const TreeNodeFactory& nodeFactory);
size_t GBT_count_leafs(const GBT_TREE *tree);
GB_ERROR GBT_is_invalid(const GBT_TREE *tree);
GB_ERROR GBT_link_tree(GBT_TREE *tree, GBDATA *gb_main, bool show_status, int *zombies, int *duplicates);
void GBT_unlink_tree(GBT_TREE *tree);
GBDATA *GBT_find_tree(GBDATA *gb_main, const char *tree_name);
GBDATA *GBT_find_largest_tree(GBDATA *gb_main);
GBDATA *GBT_tree_infrontof(GBDATA *gb_tree);
GBDATA *GBT_tree_behind(GBDATA *gb_tree);
GBDATA *GBT_find_top_tree(GBDATA *gb_main);
GBDATA *GBT_find_bottom_tree(GBDATA *gb_main);
const char *GBT_existing_tree(GBDATA *gb_main, const char *tree_name);
GBDATA *GBT_find_next_tree(GBDATA *gb_tree);
const char *GBT_get_tree_name(GBDATA *gb_tree);
GB_ERROR GBT_check_tree_name(const char *tree_name);
const char *GBT_name_of_largest_tree(GBDATA *gb_main);
const char *GBT_name_of_bottom_tree(GBDATA *gb_main);
const char *GBT_tree_info_string(GBDATA *gb_main, const char *tree_name, int maxTreeNameLen);
long GBT_size_of_tree(GBDATA *gb_main, const char *tree_name);
void GBT_get_tree_names(ConstStrArray& names, GBDATA *gb_main, bool sorted);
NOT4PERL GB_ERROR GBT_move_tree(GBDATA *gb_moved_tree, GBT_ORDER_MODE mode, GBDATA *gb_target_tree);
GB_ERROR GBT_copy_tree(GBDATA *gb_main, const char *source_name, const char *dest_name);
GB_ERROR GBT_rename_tree(GBDATA *gb_main, const char *source_name, const char *dest_name);
GB_CSTR *GBT_get_names_of_species_in_tree(const GBT_TREE *tree, size_t *count);
char *GBT_tree_2_newick(const GBT_TREE *tree, NewickFormat format);
#else
#error ad_t_prot.h included twice
#endif /* AD_T_PROT_H */
|
