source: trunk/ARBDB/ad_t_prot.h

Last change on this file was 19500, checked in by westram, 10 months ago
  • rename GBT_create_alignment → GBT_create_new_alignment.
  • restore old GBT_create_alignment flavor used before r19146 for binary compatibility.
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 12.2 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, GB_TYPES type, const char *keypath);
21GB_ERROR GBT_add_new_species_changekey(GBDATA *gb_main, const char *name, GB_TYPES type);
22GB_ERROR GBT_add_new_gene_changekey(GBDATA *gb_main, const char *name, GB_TYPES type);
23GB_ERROR GBT_add_new_experiment_changekey(GBDATA *gb_main, const char *name, GB_TYPES type);
24GB_ERROR GBT_add_new_changekey(GBDATA *gb_main, const char *name, int type) __ATTR__DEPRECATED_TODO("obsolete. use GBT_add_new_species_changekey() instead");
25GB_ERROR GBT_add_alignment_changekeys(GBDATA *gb_main, const char *ali);
26GB_ERROR GBT_write_int_converted(GBDATA *gb_int_writable, const char *data, size_t *rounded);
27GB_ERROR GBT_write_float_converted(GBDATA *gb_float_writable, const char *data);
28GB_ERROR GBT_convert_changekey(GBDATA *gb_main, const char *name, GB_TYPES target_type);
29
30/* adRevCompl.cxx */
31char *GBT_reverseNucSequence(const char *s, int len);
32char *GBT_complementNucSequence(const char *s, int len, char T_or_U);
33NOT4PERL GB_ERROR GBT_determine_T_or_U(GB_alignment_type alignment_type, char *T_or_U, const char *supposed_target);
34NOT4PERL void GBT_reverseComplementNucSequence(char *seq, long length, char T_or_U);
35
36/* adali.cxx */
37GBDATA *GBT_get_presets(GBDATA *gb_main);
38int GBT_count_alignments(GBDATA *gb_main);
39GB_ERROR GBT_check_data(GBDATA *Main, const char *alignment_name);
40void GBT_get_alignment_names(ConstStrArray& names, GBDATA *gbd);
41GB_ERROR GBT_check_alignment_name(const char *alignment_name);
42GBDATA *GBT_create_new_alignment(GBDATA *gb_main, const char *name, long len, long aligned, long security, const char *type, const char *why_created);
43GBDATA *GBT_create_alignment(GBDATA *gb_main, const char *name, long len, long aligned, long security, const char *type) __ATTR__DEPRECATED_TODO("better use GBT_create_new_alignment()");
44GB_ERROR GBT_copy_alignment(GBDATA *gbMain, const char *source, const char *dest);
45GB_ERROR GBT_rename_alignment(GBDATA *gbMain, const char *source, const char *dest);
46GB_ERROR GBT_delete_alignment(GBDATA *gbMain, const char *source);
47NOT4PERL 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()");
48NOT4PERL GBDATA *GBT_create_sequence_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type, int security_write);
49GBDATA *GBT_gen_accession_number(GBDATA *gb_species, const char *ali_name);
50int GBT_is_partial(GBDATA *gb_species, int default_value, bool define_if_undef);
51GBDATA *GBT_find_sequence(GBDATA *gb_species, const char *aliname);
52char *GBT_get_default_alignment(GBDATA *gb_main);
53char *GBT_get_startup_alignment(GBDATA *gb_main);
54GB_ERROR GBT_set_default_alignment(GBDATA *gb_main, const char *alignment_name);
55GB_ERROR GBT_set_startup_alignment(GBDATA *gb_main, const char *alignment_name);
56GBDATA *GBT_get_alignment(GBDATA *gb_main, const char *aliname);
57long GBT_get_alignment_len(GBDATA *gb_main, const char *aliname);
58GB_ERROR GBT_set_alignment_len(GBDATA *gb_main, const char *aliname, long new_len);
59char *GBT_get_alignment_type_string(GBDATA *gb_main, const char *aliname);
60GB_alignment_type GBT_get_alignment_type(GBDATA *gb_main, const char *aliname);
61bool GBT_is_alignment_protein(GBDATA *gb_main, const char *alignment_name);
62NOT4PERL char *GBT_read_gene_sequence_and_length(GBDATA *gb_gene, bool use_revComplement, char partSeparator, size_t *gene_length);
63char *GBT_read_gene_sequence(GBDATA *gb_gene, bool use_revComplement, char partSeparator);
64
65/* aditem.cxx */
66GBDATA *GBT_find_or_create_item_rel_item_data(GBDATA *gb_item_data, const char *itemname, const char *id_field, const char *id, bool markCreated);
67GBDATA *GBT_find_or_create_species_rel_species_data(GBDATA *gb_species_data, const char *name, bool markCreated);
68GBDATA *GBT_find_or_create_species(GBDATA *gb_main, const char *name, bool markCreated);
69GBDATA *GBT_find_or_create_SAI(GBDATA *gb_main, const char *name);
70GBDATA *GBT_find_item_rel_item_data(GBDATA *gb_item_data, const char *id_field, const char *id_value);
71GBDATA *GBT_expect_item_rel_item_data(GBDATA *gb_item_data, const char *id_field, const char *id_value);
72GBDATA *GBT_get_species_data(GBDATA *gb_main);
73GBDATA *GBT_first_marked_species_rel_species_data(GBDATA *gb_species_data);
74GBDATA *GBT_first_marked_species(GBDATA *gb_main);
75GBDATA *GBT_next_marked_species(GBDATA *gb_species);
76GBDATA *GBT_first_species_rel_species_data(GBDATA *gb_species_data);
77GBDATA *GBT_first_species(GBDATA *gb_main);
78GBDATA *GBT_next_species(GBDATA *gb_species);
79GBDATA *GBT_find_species_rel_species_data(GBDATA *gb_species_data, const char *name);
80GBDATA *GBT_expect_species_rel_species_data(GBDATA *gb_species_data, const char *name);
81GBDATA *GBT_find_species(GBDATA *gb_main, const char *name);
82GBDATA *GBT_expect_species(GBDATA *gb_main, const char *name);
83GBDATA *GBT_get_SAI_data(GBDATA *gb_main);
84GBDATA *GBT_first_SAI_rel_SAI_data(GBDATA *gb_sai_data);
85GBDATA *GBT_first_SAI(GBDATA *gb_main);
86GBDATA *GBT_next_SAI(GBDATA *gb_sai);
87GBDATA *GBT_find_SAI_rel_SAI_data(GBDATA *gb_sai_data, const char *name);
88GBDATA *GBT_expect_SAI_rel_SAI_data(GBDATA *gb_sai_data, const char *name);
89GBDATA *GBT_find_SAI(GBDATA *gb_main, const char *name);
90GBDATA *GBT_expect_SAI(GBDATA *gb_main, const char *name);
91long GBT_get_species_count(GBDATA *gb_main);
92long GBT_get_SAI_count(GBDATA *gb_main);
93char *GBT_create_unique_species_name(GBDATA *gb_main, const char *default_name);
94long GBT_mark_all(GBDATA *gb_main, int flag);
95long GBT_mark_all_that(GBDATA *gb_main, int flag, bool (*condition)(GBDATA *, void *), void *cd);
96long GBT_count_marked_species(GBDATA *gb_main);
97char *GBT_store_marked_species(GBDATA *gb_main, bool unmark_all);
98NOT4PERL GB_ERROR GBT_with_stored_species(GBDATA *gb_main, const char *stored, species_callback doit, int *clientdata);
99GB_ERROR GBT_restore_marked_species(GBDATA *gb_main, const char *stored_marked);
100GB_CSTR GBT_get_name_or_description(GBDATA *gb_item);
101const char *GBT_get_name(GBDATA *gb_item);
102NOT4PERL GB_CSTR GBT_read_name(GBDATA *gb_item) __ATTR__DEPRECATED_TODO("please use GBT_get_name or GBT_get_name_or_description()");
103GBDATA **GBT_gen_species_array(GBDATA *gb_main, long *speciesCountPtr);
104
105/* adname.cxx */
106GB_ERROR GBT_begin_rename_session(GBDATA *gb_main, int all_flag);
107GB_ERROR GBT_rename_species(const char *oldname, const char *newname, bool ignore_protection);
108GB_ERROR GBT_abort_rename_session(void);
109GB_ERROR GBT_commit_rename_session(void) __ATTR__USERESULT;
110
111/* adseqcompr.cxx */
112GB_ERROR GBT_compress_sequence_tree2(GBDATA *gbd, const char *tree_name, const char *ali_name) __ATTR__USERESULT;
113void GBT_compression_test(struct Unfixed_cb_parameter *, GBDATA *gb_main);
114
115/* adtools.cxx */
116GBDATA *GBT_create(GBDATA *father, const char *key, long delete_level);
117GBDATA *GBT_find_or_create(GBDATA *father, const char *key, long delete_level);
118char *GBT_get_default_helix(GBDATA *);
119char *GBT_get_default_helix_nr(GBDATA *);
120char *GBT_get_default_ref(GBDATA *);
121void GBT_scan_db(StrArray& fieldNames, GBDATA *gbd, const char *datapath);
122void GBT_install_message_handler(GBDATA *gb_main);
123void GBT_message(GBDATA *gb_main, const char *msg);
124char *GBT_read_string(GBDATA *gb_container, const char *fieldpath);
125char *GBT_read_as_string(GBDATA *gb_container, const char *fieldpath);
126const char *GBT_read_char_pntr(GBDATA *gb_container, const char *fieldpath);
127NOT4PERL long *GBT_read_int(GBDATA *gb_container, const char *fieldpath);
128NOT4PERL float *GBT_read_float(GBDATA *gb_container, const char *fieldpath);
129char *GBT_readOrCreate_string(GBDATA *gb_container, const char *fieldpath, const char *default_value);
130const char *GBT_readOrCreate_char_pntr(GBDATA *gb_container, const char *fieldpath, const char *default_value);
131NOT4PERL long *GBT_readOrCreate_int(GBDATA *gb_container, const char *fieldpath, long default_value);
132NOT4PERL float *GBT_readOrCreate_float(GBDATA *gb_container, const char *fieldpath, float default_value);
133GB_ERROR GBT_write_string(GBDATA *gb_container, const char *fieldpath, const char *content);
134GB_ERROR GBT_write_int(GBDATA *gb_container, const char *fieldpath, long content);
135GB_ERROR GBT_write_byte(GBDATA *gb_container, const char *fieldpath, unsigned char content);
136GB_ERROR GBT_write_float(GBDATA *gb_container, const char *fieldpath, float content);
137GBDATA *GBT_open(const char *path, const char *opent);
138GB_ERROR GB_set_macro_error(GBDATA *gb_main, const char *curr_error);
139GB_ERROR GB_get_macro_error(GBDATA *gb_main);
140GB_ERROR GB_clear_macro_error(GBDATA *gb_main);
141NOT4PERL GB_ERROR GBT_remote_action_with_timeout(GBDATA *gb_main, const char *application, const char *action_name, const class ARB_timeout *timeout, bool verbose);
142GB_ERROR GBT_remote_action(GBDATA *gb_main, const char *application, const char *action_name);
143GB_ERROR GBT_remote_awar(GBDATA *gb_main, const char *application, const char *awar_name, const char *value);
144GB_ERROR GBT_remote_read_awar(GBDATA *gb_main, const char *application, const char *awar_name);
145const char *GBT_relativeMacroname(const char *macro_name);
146GB_ERROR GBT_macro_execute(const char *macro_name, bool loop_marked, bool run_async);
147
148/* adtree.cxx */
149GBDATA *GBT_get_tree_data(GBDATA *gb_main);
150TreeNode *GBT_remove_leafs(TreeNode *tree, GBT_TreeRemoveType mode, const GB_HASH *species_hash, int *removed, int *groups_removed);
151GB_ERROR GBT_write_group_name(GBDATA *gb_group_name, const char *new_group_name, bool pedantic);
152GB_ERROR GBT_write_name_to_groupData(GBDATA *gb_group, bool createNameEntry, const char *new_group_name, bool pedantic);
153GB_ERROR GBT_write_tree(GBDATA *gb_main, const char *tree_name, TreeNode *tree);
154GB_ERROR GBT_overwrite_tree(GBDATA *gb_tree, TreeNode *tree);
155GB_ERROR GBT_write_tree_remark(GBDATA *gb_main, const char *tree_name, const char *remark);
156GB_ERROR GBT_log_to_tree_remark(GBDATA *gb_tree, const char *log_entry, bool stamp);
157GB_ERROR GBT_log_to_named_trees_remark(GBDATA *gb_main, const char *tree_name, const char *log_entry, bool stamp);
158GB_ERROR GBT_write_tree_with_remark(GBDATA *gb_main, const char *tree_name, TreeNode *tree, const char *remark);
159TreeNode *GBT_read_tree_and_size(GBDATA *gb_main, const char *tree_name, TreeRoot *troot, int *tree_size);
160TreeNode *GBT_read_tree(GBDATA *gb_main, const char *tree_name, TreeRoot *troot);
161size_t GBT_count_leafs(const TreeNode *tree);
162GB_ERROR GBT_is_invalid(const TreeNode *tree);
163GB_ERROR GBT_link_tree(TreeNode *tree, GBDATA *gb_main, bool show_status, int *zombies, int *duplicates);
164void GBT_unlink_tree(TreeNode *tree);
165GBDATA *GBT_find_tree(GBDATA *gb_main, const char *tree_name);
166GBDATA *GBT_tree_infrontof(GBDATA *gb_tree);
167GBDATA *GBT_tree_behind(GBDATA *gb_tree);
168GBDATA *GBT_find_top_tree(GBDATA *gb_main);
169GBDATA *GBT_find_bottom_tree(GBDATA *gb_main);
170const char *GBT_existing_tree(GBDATA *gb_main, const char *tree_name);
171GBDATA *GBT_find_next_tree(GBDATA *gb_tree);
172const char *GBT_get_tree_name(GBDATA *gb_tree);
173GB_ERROR GBT_check_tree_name(const char *tree_name);
174const char *GBT_name_of_largest_tree(GBDATA *gb_main);
175const char *GBT_name_of_bottom_tree(GBDATA *gb_main);
176const char *GBT_tree_info_string(GBDATA *gb_main, const char *tree_name, int maxTreeNameLen);
177long GBT_size_of_tree(GBDATA *gb_main, const char *tree_name);
178void GBT_get_tree_names(ConstStrArray& names, GBDATA *gb_main, bool sorted);
179NOT4PERL GB_ERROR GBT_move_tree(GBDATA *gb_moved_tree, GBT_ORDER_MODE mode, GBDATA *gb_target_tree);
180GB_ERROR GBT_copy_tree(GBDATA *gb_main, const char *source_name, const char *dest_name);
181GB_ERROR GBT_rename_tree(GBDATA *gb_main, const char *source_name, const char *dest_name);
182GB_CSTR *GBT_get_names_of_species_in_tree(const TreeNode *tree, size_t *count);
183char *GBT_tree_2_newick(const TreeNode *tree, NewickFormat format, bool compact);
184
185#else
186#error ad_t_prot.h included twice
187#endif /* AD_T_PROT_H */
Note: See TracBrowser for help on using the repository browser.