source: branches/help/ARBDB/ad_t_prot.h

Last change on this file was 18752, checked in by westram, 3 years ago
  • eliminate obsolete GBT_read_name from perl interface
    • To fix your skript you have to replace BIO::read_name by
      • BIO::get_name or
      • BIO::get_name_or_description (=1:1 replacement).
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 11.5 KB
Line 
1/* ARB toolkit.
2 *
3 * This file is generated by aisc_mkpt.
4 * Any changes you make here will be overwritten later!
5 */
6
7#ifndef AD_T_PROT_H
8#define AD_T_PROT_H
9
10/* define ARB attributes: */
11#ifndef ATTRIBUTES_H
12# include <attributes.h>
13#endif
14
15
16/* adChangeKey.cxx */
17GBDATA *GBT_get_changekey(GBDATA *gb_main, const char *key, const char *change_key_path);
18GB_TYPES GBT_get_type_of_changekey(GBDATA *gb_main, const char *field_name, const char *change_key_path);
19GBDATA *GBT_searchOrCreate_itemfield_according_to_changekey(GBDATA *gb_item, const char *field_name, const char *change_key_path);
20GB_ERROR GBT_add_new_changekey_to_keypath(GBDATA *gb_main, const char *name, int type, const char *keypath);
21GB_ERROR GBT_add_new_changekey(GBDATA *gb_main, const char *name, int type);
22GB_ERROR GBT_add_new_gene_changekey(GBDATA *gb_main, const char *name, int type);
23GB_ERROR GBT_add_new_experiment_changekey(GBDATA *gb_main, const char *name, int type);
24GB_ERROR GBT_write_int_converted(GBDATA *gb_int_writable, const char *data, size_t *rounded);
25GB_ERROR GBT_write_float_converted(GBDATA *gb_float_writable, const char *data);
26GB_ERROR GBT_convert_changekey(GBDATA *gb_main, const char *name, GB_TYPES target_type);
27
28/* adRevCompl.cxx */
29char *GBT_reverseNucSequence(const char *s, int len);
30char *GBT_complementNucSequence(const char *s, int len, char T_or_U);
31NOT4PERL GB_ERROR GBT_determine_T_or_U(GB_alignment_type alignment_type, char *T_or_U, const char *supposed_target);
32NOT4PERL void GBT_reverseComplementNucSequence(char *seq, long length, char T_or_U);
33
34/* adali.cxx */
35GBDATA *GBT_get_presets(GBDATA *gb_main);
36int GBT_count_alignments(GBDATA *gb_main);
37GB_ERROR GBT_check_data(GBDATA *Main, const char *alignment_name);
38void GBT_get_alignment_names(ConstStrArray& names, GBDATA *gbd);
39GB_ERROR GBT_check_alignment_name(const char *alignment_name);
40GBDATA *GBT_create_alignment(GBDATA *gbd, const char *name, long len, long aligned, long security, const char *type);
41GB_ERROR GBT_rename_alignment(GBDATA *gbMain, const char *source, const char *dest, bool copy, bool delete_src);
42NOT4PERL 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()");
43NOT4PERL GBDATA *GBT_create_sequence_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type, int security_write);
44GBDATA *GBT_gen_accession_number(GBDATA *gb_species, const char *ali_name);
45int GBT_is_partial(GBDATA *gb_species, int default_value, bool define_if_undef);
46GBDATA *GBT_find_sequence(GBDATA *gb_species, const char *aliname);
47char *GBT_get_default_alignment(GBDATA *gb_main);
48GB_ERROR GBT_set_default_alignment(GBDATA *gb_main, const char *alignment_name);
49GBDATA *GBT_get_alignment(GBDATA *gb_main, const char *aliname);
50long GBT_get_alignment_len(GBDATA *gb_main, const char *aliname);
51GB_ERROR GBT_set_alignment_len(GBDATA *gb_main, const char *aliname, long new_len);
52char *GBT_get_alignment_type_string(GBDATA *gb_main, const char *aliname);
53GB_alignment_type GBT_get_alignment_type(GBDATA *gb_main, const char *aliname);
54bool GBT_is_alignment_protein(GBDATA *gb_main, const char *alignment_name);
55NOT4PERL char *GBT_read_gene_sequence_and_length(GBDATA *gb_gene, bool use_revComplement, char partSeparator, size_t *gene_length);
56char *GBT_read_gene_sequence(GBDATA *gb_gene, bool use_revComplement, char partSeparator);
57
58/* aditem.cxx */
59GBDATA *GBT_find_or_create_item_rel_item_data(GBDATA *gb_item_data, const char *itemname, const char *id_field, const char *id, bool markCreated);
60GBDATA *GBT_find_or_create_species_rel_species_data(GBDATA *gb_species_data, const char *name, bool markCreated);
61GBDATA *GBT_find_or_create_species(GBDATA *gb_main, const char *name, bool markCreated);
62GBDATA *GBT_find_or_create_SAI(GBDATA *gb_main, const char *name);
63GBDATA *GBT_find_item_rel_item_data(GBDATA *gb_item_data, const char *id_field, const char *id_value);
64GBDATA *GBT_expect_item_rel_item_data(GBDATA *gb_item_data, const char *id_field, const char *id_value);
65GBDATA *GBT_get_species_data(GBDATA *gb_main);
66GBDATA *GBT_first_marked_species_rel_species_data(GBDATA *gb_species_data);
67GBDATA *GBT_first_marked_species(GBDATA *gb_main);
68GBDATA *GBT_next_marked_species(GBDATA *gb_species);
69GBDATA *GBT_first_species_rel_species_data(GBDATA *gb_species_data);
70GBDATA *GBT_first_species(GBDATA *gb_main);
71GBDATA *GBT_next_species(GBDATA *gb_species);
72GBDATA *GBT_find_species_rel_species_data(GBDATA *gb_species_data, const char *name);
73GBDATA *GBT_expect_species_rel_species_data(GBDATA *gb_species_data, const char *name);
74GBDATA *GBT_find_species(GBDATA *gb_main, const char *name);
75GBDATA *GBT_expect_species(GBDATA *gb_main, const char *name);
76GBDATA *GBT_get_SAI_data(GBDATA *gb_main);
77GBDATA *GBT_first_SAI_rel_SAI_data(GBDATA *gb_sai_data);
78GBDATA *GBT_first_SAI(GBDATA *gb_main);
79GBDATA *GBT_next_SAI(GBDATA *gb_sai);
80GBDATA *GBT_find_SAI_rel_SAI_data(GBDATA *gb_sai_data, const char *name);
81GBDATA *GBT_expect_SAI_rel_SAI_data(GBDATA *gb_sai_data, const char *name);
82GBDATA *GBT_find_SAI(GBDATA *gb_main, const char *name);
83GBDATA *GBT_expect_SAI(GBDATA *gb_main, const char *name);
84long GBT_get_species_count(GBDATA *gb_main);
85long GBT_get_SAI_count(GBDATA *gb_main);
86char *GBT_create_unique_species_name(GBDATA *gb_main, const char *default_name);
87void GBT_mark_all(GBDATA *gb_main, int flag);
88void GBT_mark_all_that(GBDATA *gb_main, int flag, bool (*condition)(GBDATA *, void *), void *cd);
89long GBT_count_marked_species(GBDATA *gb_main);
90char *GBT_store_marked_species(GBDATA *gb_main, bool unmark_all);
91NOT4PERL GB_ERROR GBT_with_stored_species(GBDATA *gb_main, const char *stored, species_callback doit, int *clientdata);
92GB_ERROR GBT_restore_marked_species(GBDATA *gb_main, const char *stored_marked);
93GB_CSTR GBT_get_name_or_description(GBDATA *gb_item);
94const char *GBT_get_name(GBDATA *gb_item);
95NOT4PERL GB_CSTR GBT_read_name(GBDATA *gb_item) __ATTR__DEPRECATED_TODO("please use GBT_get_name or GBT_get_name_or_description()");
96GBDATA **GBT_gen_species_array(GBDATA *gb_main, long *speciesCountPtr);
97
98/* adname.cxx */
99GB_ERROR GBT_begin_rename_session(GBDATA *gb_main, int all_flag);
100GB_ERROR GBT_rename_species(const char *oldname, const char *newname, bool ignore_protection);
101GB_ERROR GBT_abort_rename_session(void);
102GB_ERROR GBT_commit_rename_session(void) __ATTR__USERESULT;
103
104/* adseqcompr.cxx */
105GB_ERROR GBT_compress_sequence_tree2(GBDATA *gbd, const char *tree_name, const char *ali_name) __ATTR__USERESULT;
106void GBT_compression_test(struct Unfixed_cb_parameter *, GBDATA *gb_main);
107
108/* adtools.cxx */
109GBDATA *GBT_create(GBDATA *father, const char *key, long delete_level);
110GBDATA *GBT_find_or_create(GBDATA *father, const char *key, long delete_level);
111char *GBT_get_default_helix(GBDATA *);
112char *GBT_get_default_helix_nr(GBDATA *);
113char *GBT_get_default_ref(GBDATA *);
114void GBT_scan_db(StrArray& fieldNames, GBDATA *gbd, const char *datapath);
115void GBT_install_message_handler(GBDATA *gb_main);
116void GBT_message(GBDATA *gb_main, const char *msg);
117char *GBT_read_string(GBDATA *gb_container, const char *fieldpath);
118char *GBT_read_as_string(GBDATA *gb_container, const char *fieldpath);
119const char *GBT_read_char_pntr(GBDATA *gb_container, const char *fieldpath);
120NOT4PERL long *GBT_read_int(GBDATA *gb_container, const char *fieldpath);
121NOT4PERL float *GBT_read_float(GBDATA *gb_container, const char *fieldpath);
122char *GBT_readOrCreate_string(GBDATA *gb_container, const char *fieldpath, const char *default_value);
123const char *GBT_readOrCreate_char_pntr(GBDATA *gb_container, const char *fieldpath, const char *default_value);
124NOT4PERL long *GBT_readOrCreate_int(GBDATA *gb_container, const char *fieldpath, long default_value);
125NOT4PERL float *GBT_readOrCreate_float(GBDATA *gb_container, const char *fieldpath, float default_value);
126GB_ERROR GBT_write_string(GBDATA *gb_container, const char *fieldpath, const char *content);
127GB_ERROR GBT_write_int(GBDATA *gb_container, const char *fieldpath, long content);
128GB_ERROR GBT_write_byte(GBDATA *gb_container, const char *fieldpath, unsigned char content);
129GB_ERROR GBT_write_float(GBDATA *gb_container, const char *fieldpath, float content);
130GBDATA *GBT_open(const char *path, const char *opent);
131GB_ERROR GB_set_macro_error(GBDATA *gb_main, const char *curr_error);
132GB_ERROR GB_get_macro_error(GBDATA *gb_main);
133GB_ERROR GB_clear_macro_error(GBDATA *gb_main);
134NOT4PERL GB_ERROR GBT_remote_action_with_timeout(GBDATA *gb_main, const char *application, const char *action_name, const class ARB_timeout *timeout, bool verbose);
135GB_ERROR GBT_remote_action(GBDATA *gb_main, const char *application, const char *action_name);
136GB_ERROR GBT_remote_awar(GBDATA *gb_main, const char *application, const char *awar_name, const char *value);
137GB_ERROR GBT_remote_read_awar(GBDATA *gb_main, const char *application, const char *awar_name);
138const char *GBT_relativeMacroname(const char *macro_name);
139GB_ERROR GBT_macro_execute(const char *macro_name, bool loop_marked, bool run_async);
140
141/* adtree.cxx */
142GBDATA *GBT_get_tree_data(GBDATA *gb_main);
143TreeNode *GBT_remove_leafs(TreeNode *tree, GBT_TreeRemoveType mode, const GB_HASH *species_hash, int *removed, int *groups_removed);
144GB_ERROR GBT_write_group_name(GBDATA *gb_group_name, const char *new_group_name, bool pedantic);
145GB_ERROR GBT_write_name_to_groupData(GBDATA *gb_group, bool createNameEntry, const char *new_group_name, bool pedantic);
146GB_ERROR GBT_write_tree(GBDATA *gb_main, const char *tree_name, TreeNode *tree);
147GB_ERROR GBT_overwrite_tree(GBDATA *gb_tree, TreeNode *tree);
148GB_ERROR GBT_write_tree_remark(GBDATA *gb_main, const char *tree_name, const char *remark);
149GB_ERROR GBT_log_to_tree_remark(GBDATA *gb_tree, const char *log_entry, bool stamp);
150GB_ERROR GBT_log_to_named_trees_remark(GBDATA *gb_main, const char *tree_name, const char *log_entry, bool stamp);
151GB_ERROR GBT_write_tree_with_remark(GBDATA *gb_main, const char *tree_name, TreeNode *tree, const char *remark);
152TreeNode *GBT_read_tree_and_size(GBDATA *gb_main, const char *tree_name, TreeRoot *troot, int *tree_size);
153TreeNode *GBT_read_tree(GBDATA *gb_main, const char *tree_name, TreeRoot *troot);
154size_t GBT_count_leafs(const TreeNode *tree);
155GB_ERROR GBT_is_invalid(const TreeNode *tree);
156GB_ERROR GBT_link_tree(TreeNode *tree, GBDATA *gb_main, bool show_status, int *zombies, int *duplicates);
157void GBT_unlink_tree(TreeNode *tree);
158GBDATA *GBT_find_tree(GBDATA *gb_main, const char *tree_name);
159GBDATA *GBT_tree_infrontof(GBDATA *gb_tree);
160GBDATA *GBT_tree_behind(GBDATA *gb_tree);
161GBDATA *GBT_find_top_tree(GBDATA *gb_main);
162GBDATA *GBT_find_bottom_tree(GBDATA *gb_main);
163const char *GBT_existing_tree(GBDATA *gb_main, const char *tree_name);
164GBDATA *GBT_find_next_tree(GBDATA *gb_tree);
165const char *GBT_get_tree_name(GBDATA *gb_tree);
166GB_ERROR GBT_check_tree_name(const char *tree_name);
167const char *GBT_name_of_largest_tree(GBDATA *gb_main);
168const char *GBT_name_of_bottom_tree(GBDATA *gb_main);
169const char *GBT_tree_info_string(GBDATA *gb_main, const char *tree_name, int maxTreeNameLen);
170long GBT_size_of_tree(GBDATA *gb_main, const char *tree_name);
171void GBT_get_tree_names(ConstStrArray& names, GBDATA *gb_main, bool sorted);
172NOT4PERL GB_ERROR GBT_move_tree(GBDATA *gb_moved_tree, GBT_ORDER_MODE mode, GBDATA *gb_target_tree);
173GB_ERROR GBT_copy_tree(GBDATA *gb_main, const char *source_name, const char *dest_name);
174GB_ERROR GBT_rename_tree(GBDATA *gb_main, const char *source_name, const char *dest_name);
175GB_CSTR *GBT_get_names_of_species_in_tree(const TreeNode *tree, size_t *count);
176char *GBT_tree_2_newick(const TreeNode *tree, NewickFormat format, bool compact);
177
178#else
179#error ad_t_prot.h included twice
180#endif /* AD_T_PROT_H */
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