ARB
ad_t_prot.h
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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 */
17 GBDATA *GBT_get_changekey(GBDATA *gb_main, const char *key, const char *change_key_path);
18 GB_TYPES GBT_get_type_of_changekey(GBDATA *gb_main, const char *field_name, const char *change_key_path);
19 GBDATA *GBT_searchOrCreate_itemfield_according_to_changekey(GBDATA *gb_item, const char *field_name, const char *change_key_path);
20 GB_ERROR GBT_add_new_changekey_to_keypath(GBDATA *gb_main, const char *name, int type, const char *keypath);
21 GB_ERROR GBT_add_new_changekey(GBDATA *gb_main, const char *name, int type);
22 GB_ERROR GBT_add_new_gene_changekey(GBDATA *gb_main, const char *name, int type);
24 GB_ERROR GBT_write_int_converted(GBDATA *gb_int_writable, const char *data, size_t *rounded);
25 GB_ERROR GBT_write_float_converted(GBDATA *gb_float_writable, const char *data);
26 GB_ERROR GBT_convert_changekey(GBDATA *gb_main, const char *name, GB_TYPES target_type);
27 
28 /* adRevCompl.cxx */
29 char *GBT_reverseNucSequence(const char *s, int len);
30 char *GBT_complementNucSequence(const char *s, int len, char T_or_U);
31 NOT4PERL GB_ERROR GBT_determine_T_or_U(GB_alignment_type alignment_type, char *T_or_U, const char *supposed_target);
32 NOT4PERL void GBT_reverseComplementNucSequence(char *seq, long length, char T_or_U);
33 
34 /* adali.cxx */
37 GB_ERROR GBT_check_data(GBDATA *Main, const char *alignment_name);
40 GBDATA *GBT_create_alignment(GBDATA *gbd, const char *name, long len, long aligned, long security, const char *type);
41 GB_ERROR GBT_rename_alignment(GBDATA *gbMain, const char *source, const char *dest, int copy, int dele);
42 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()");
43 NOT4PERL GBDATA *GBT_create_sequence_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type, int security_write);
44 GBDATA *GBT_gen_accession_number(GBDATA *gb_species, const char *ali_name);
45 int GBT_is_partial(GBDATA *gb_species, int default_value, bool define_if_undef);
46 GBDATA *GBT_find_sequence(GBDATA *gb_species, const char *aliname);
49 GBDATA *GBT_get_alignment(GBDATA *gb_main, const char *aliname);
50 long GBT_get_alignment_len(GBDATA *gb_main, const char *aliname);
51 GB_ERROR GBT_set_alignment_len(GBDATA *gb_main, const char *aliname, long new_len);
52 char *GBT_get_alignment_type_string(GBDATA *gb_main, const char *aliname);
55 NOT4PERL char *GBT_read_gene_sequence_and_length(GBDATA *gb_gene, bool use_revComplement, char partSeparator, size_t *gene_length);
56 char *GBT_read_gene_sequence(GBDATA *gb_gene, bool use_revComplement, char partSeparator);
57 
58 /* aditem.cxx */
59 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);
60 GBDATA *GBT_find_or_create_species_rel_species_data(GBDATA *gb_species_data, const char *name, bool markCreated);
61 GBDATA *GBT_find_or_create_species(GBDATA *gb_main, const char *name, bool markCreated);
62 GBDATA *GBT_find_or_create_SAI(GBDATA *gb_main, const char *name);
63 GBDATA *GBT_find_item_rel_item_data(GBDATA *gb_item_data, const char *id_field, const char *id_value);
64 GBDATA *GBT_expect_item_rel_item_data(GBDATA *gb_item_data, const char *id_field, const char *id_value);
71 GBDATA *GBT_next_species(GBDATA *gb_species);
74 GBDATA *GBT_find_species(GBDATA *gb_main, const char *name);
75 GBDATA *GBT_expect_species(GBDATA *gb_main, const char *name);
79 GBDATA *GBT_next_SAI(GBDATA *gb_sai);
80 GBDATA *GBT_find_SAI_rel_SAI_data(GBDATA *gb_sai_data, const char *name);
81 GBDATA *GBT_expect_SAI_rel_SAI_data(GBDATA *gb_sai_data, const char *name);
82 GBDATA *GBT_find_SAI(GBDATA *gb_main, const char *name);
83 GBDATA *GBT_expect_SAI(GBDATA *gb_main, const char *name);
86 char *GBT_create_unique_species_name(GBDATA *gb_main, const char *default_name);
87 void GBT_mark_all(GBDATA *gb_main, int flag);
88 void GBT_mark_all_that(GBDATA *gb_main, int flag, bool (*condition)(GBDATA *, void *), void *cd);
89 long GBT_count_marked_species(GBDATA *gb_main);
90 char *GBT_store_marked_species(GBDATA *gb_main, bool unmark_all);
91 NOT4PERL GB_ERROR GBT_with_stored_species(GBDATA *gb_main, const char *stored, species_callback doit, int *clientdata);
92 GB_ERROR GBT_restore_marked_species(GBDATA *gb_main, const char *stored_marked);
94 const char *GBT_get_name(GBDATA *gb_item);
95 GB_CSTR GBT_read_name(GBDATA *gb_item) __ATTR__DEPRECATED_TODO("please use GBT_get_name or GBT_get_name_or_description()");
96 GBDATA **GBT_gen_species_array(GBDATA *gb_main, long *speciesCountPtr);
97 
98 /* adname.cxx */
100 GB_ERROR GBT_rename_species(const char *oldname, const char *newname, bool ignore_protection);
103 
104 /* adseqcompr.cxx */
105 GB_ERROR GBT_compress_sequence_tree2(GBDATA *gbd, const char *tree_name, const char *ali_name) __ATTR__USERESULT;
106 void GBT_compression_test(struct Unfixed_cb_parameter *, GBDATA *gb_main);
107 
108 /* adtools.cxx */
109 GBDATA *GBT_create(GBDATA *father, const char *key, long delete_level);
110 GBDATA *GBT_find_or_create(GBDATA *father, const char *key, long delete_level);
112 char *GBT_get_default_helix_nr(GBDATA *);
113 char *GBT_get_default_ref(GBDATA *);
114 void GBT_scan_db(StrArray& fieldNames, GBDATA *gbd, const char *datapath);
115 void GBT_install_message_handler(GBDATA *gb_main);
116 void GBT_message(GBDATA *gb_main, const char *msg);
117 char *GBT_read_string(GBDATA *gb_container, const char *fieldpath);
118 char *GBT_read_as_string(GBDATA *gb_container, const char *fieldpath);
119 const char *GBT_read_char_pntr(GBDATA *gb_container, const char *fieldpath);
120 NOT4PERL long *GBT_read_int(GBDATA *gb_container, const char *fieldpath);
121 NOT4PERL float *GBT_read_float(GBDATA *gb_container, const char *fieldpath);
122 char *GBT_readOrCreate_string(GBDATA *gb_container, const char *fieldpath, const char *default_value);
123 const char *GBT_readOrCreate_char_pntr(GBDATA *gb_container, const char *fieldpath, const char *default_value);
124 NOT4PERL long *GBT_readOrCreate_int(GBDATA *gb_container, const char *fieldpath, long default_value);
125 NOT4PERL float *GBT_readOrCreate_float(GBDATA *gb_container, const char *fieldpath, float default_value);
126 GB_ERROR GBT_write_string(GBDATA *gb_container, const char *fieldpath, const char *content);
127 GB_ERROR GBT_write_int(GBDATA *gb_container, const char *fieldpath, long content);
128 GB_ERROR GBT_write_byte(GBDATA *gb_container, const char *fieldpath, unsigned char content);
129 GB_ERROR GBT_write_float(GBDATA *gb_container, const char *fieldpath, float content);
130 GBDATA *GBT_open(const char *path, const char *opent);
131 GB_ERROR GB_set_macro_error(GBDATA *gb_main, const char *curr_error);
132 GB_ERROR GB_get_macro_error(GBDATA *gb_main);
133 GB_ERROR GB_clear_macro_error(GBDATA *gb_main);
134 NOT4PERL GB_ERROR GBT_remote_action_with_timeout(GBDATA *gb_main, const char *application, const char *action_name, const class ARB_timeout *timeout, bool verbose);
135 GB_ERROR GBT_remote_action(GBDATA *gb_main, const char *application, const char *action_name);
136 GB_ERROR GBT_remote_awar(GBDATA *gb_main, const char *application, const char *awar_name, const char *value);
137 GB_ERROR GBT_remote_read_awar(GBDATA *gb_main, const char *application, const char *awar_name);
138 const char *GBT_relativeMacroname(const char *macro_name);
139 GB_ERROR GBT_macro_execute(const char *macro_name, bool loop_marked, bool run_async);
140 
141 /* adtree.cxx */
142 GBDATA *GBT_get_tree_data(GBDATA *gb_main);
143 TreeNode *GBT_remove_leafs(TreeNode *tree, GBT_TreeRemoveType mode, const GB_HASH *species_hash, int *removed, int *groups_removed);
144 GB_ERROR GBT_write_group_name(GBDATA *gb_group_name, const char *new_group_name, bool pedantic);
145 GB_ERROR GBT_write_name_to_groupData(GBDATA *gb_group, bool createNameEntry, const char *new_group_name, bool pedantic);
146 GB_ERROR GBT_write_tree(GBDATA *gb_main, const char *tree_name, TreeNode *tree);
147 GB_ERROR GBT_overwrite_tree(GBDATA *gb_tree, TreeNode *tree);
148 GB_ERROR GBT_write_tree_remark(GBDATA *gb_main, const char *tree_name, const char *remark);
149 GB_ERROR GBT_log_to_tree_remark(GBDATA *gb_tree, const char *log_entry, bool stamp);
150 GB_ERROR GBT_log_to_tree_remark(GBDATA *gb_main, const char *tree_name, const char *log_entry, bool stamp);
151 GB_ERROR GBT_write_tree_with_remark(GBDATA *gb_main, const char *tree_name, TreeNode *tree, const char *remark);
152 TreeNode *GBT_read_tree_and_size(GBDATA *gb_main, const char *tree_name, TreeRoot *troot, int *tree_size);
153 TreeNode *GBT_read_tree(GBDATA *gb_main, const char *tree_name, TreeRoot *troot);
154 size_t GBT_count_leafs(const TreeNode *tree);
155 GB_ERROR GBT_is_invalid(const TreeNode *tree);
156 GB_ERROR GBT_link_tree(TreeNode *tree, GBDATA *gb_main, bool show_status, int *zombies, int *duplicates);
157 void GBT_unlink_tree(TreeNode *tree);
158 GBDATA *GBT_find_tree(GBDATA *gb_main, const char *tree_name);
159 GBDATA *GBT_tree_infrontof(GBDATA *gb_tree);
160 GBDATA *GBT_tree_behind(GBDATA *gb_tree);
161 GBDATA *GBT_find_top_tree(GBDATA *gb_main);
162 GBDATA *GBT_find_bottom_tree(GBDATA *gb_main);
163 const char *GBT_existing_tree(GBDATA *gb_main, const char *tree_name);
164 GBDATA *GBT_find_next_tree(GBDATA *gb_tree);
165 const char *GBT_get_tree_name(GBDATA *gb_tree);
166 GB_ERROR GBT_check_tree_name(const char *tree_name);
167 const char *GBT_name_of_largest_tree(GBDATA *gb_main);
168 const char *GBT_name_of_bottom_tree(GBDATA *gb_main);
169 const char *GBT_tree_info_string(GBDATA *gb_main, const char *tree_name, int maxTreeNameLen);
170 long GBT_size_of_tree(GBDATA *gb_main, const char *tree_name);
171 void GBT_get_tree_names(ConstStrArray& names, GBDATA *gb_main, bool sorted);
172 NOT4PERL GB_ERROR GBT_move_tree(GBDATA *gb_moved_tree, GBT_ORDER_MODE mode, GBDATA *gb_target_tree);
173 GB_ERROR GBT_copy_tree(GBDATA *gb_main, const char *source_name, const char *dest_name);
174 GB_ERROR GBT_rename_tree(GBDATA *gb_main, const char *source_name, const char *dest_name);
175 GB_CSTR *GBT_get_names_of_species_in_tree(const TreeNode *tree, size_t *count);
176 char *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 */
GBDATA * GBT_find_bottom_tree(GBDATA *gb_main)
Definition: adtree.cxx:1004
const char * GB_ERROR
Definition: arb_core.h:25
NOT4PERL GB_ERROR GBT_move_tree(GBDATA *gb_moved_tree, GBT_ORDER_MODE mode, GBDATA *gb_target_tree)
Definition: adtree.cxx:1194
GBDATA * GBT_first_SAI(GBDATA *gb_main)
Definition: aditem.cxx:162
size_t GBT_count_leafs(const TreeNode *tree)
Definition: adtree.cxx:796
GB_TYPES type
GBT_TreeRemoveType
Definition: arbdbt.h:31
void GBT_compression_test(struct Unfixed_cb_parameter *, GBDATA *gb_main)
GBDATA * GBT_first_marked_species(GBDATA *gb_main)
Definition: aditem.cxx:113
AliDataPtr format(AliDataPtr data, const size_t wanted_len, GB_ERROR &error)
Definition: insdel.cxx:615
GB_ERROR GBT_write_tree_with_remark(GBDATA *gb_main, const char *tree_name, TreeNode *tree, const char *remark)
Definition: adtree.cxx:524
GB_ERROR GB_set_macro_error(GBDATA *gb_main, const char *curr_error)
Definition: adtools.cxx:670
GB_ERROR GBT_rename_species(const char *oldname, const char *newname, bool ignore_protection)
Definition: adname.cxx:68
void GBT_unlink_tree(TreeNode *tree)
Definition: adtree.cxx:940
GBDATA * GBT_first_marked_species_rel_species_data(GBDATA *gb_species_data)
Definition: aditem.cxx:109
GB_ERROR GBT_restore_marked_species(GBDATA *gb_main, const char *stored_marked)
Definition: aditem.cxx:428
GBDATA * GBT_expect_item_rel_item_data(GBDATA *gb_item_data, const char *id_field, const char *id_value)
Definition: aditem.cxx:91
GBDATA ** GBT_gen_species_array(GBDATA *gb_main, long *speciesCountPtr)
Definition: aditem.cxx:467
GBDATA * GBT_expect_SAI_rel_SAI_data(GBDATA *gb_sai_data, const char *name)
Definition: aditem.cxx:174
int GBT_count_alignments(GBDATA *gb_main)
Definition: adali.cxx:33
GBDATA * GBT_expect_species_rel_species_data(GBDATA *gb_species_data, const char *name)
Definition: aditem.cxx:136
char * GBT_complementNucSequence(const char *s, int len, char T_or_U)
Definition: adRevCompl.cxx:78
GBDATA * GBT_tree_behind(GBDATA *gb_tree)
Definition: adtree.cxx:990
GB_ERROR GBT_check_alignment_name(const char *alignment_name)
Definition: adali.cxx:342
GB_ERROR GBT_macro_execute(const char *macro_name, bool loop_marked, bool run_async)
Definition: adtools.cxx:919
TreeNode * GBT_remove_leafs(TreeNode *tree, GBT_TreeRemoveType mode, const GB_HASH *species_hash, int *removed, int *groups_removed)
Definition: adtree.cxx:33
char * GBT_tree_2_newick(const TreeNode *tree, NewickFormat format, bool compact)
Definition: adtree.cxx:1353
GBDATA * GBT_get_alignment(GBDATA *gb_main, const char *aliname)
Definition: adali.cxx:684
const char * GBT_name_of_bottom_tree(GBDATA *gb_main)
Definition: adtree.cxx:1061
NOT4PERL GB_ERROR GBT_with_stored_species(GBDATA *gb_main, const char *stored, species_callback doit, int *clientdata)
Definition: aditem.cxx:386
const char * GBT_name_of_largest_tree(GBDATA *gb_main)
Definition: adtree.cxx:1057
long GBT_get_SAI_count(GBDATA *gb_main)
Definition: aditem.cxx:211
void GBT_get_alignment_names(ConstStrArray &names, GBDATA *gbd)
Definition: adali.cxx:316
char * GBT_reverseNucSequence(const char *s, int len)
Definition: adRevCompl.cxx:66
TreeNode * GBT_read_tree(GBDATA *gb_main, const char *tree_name, TreeRoot *troot)
Definition: adtree.cxx:791
GB_ERROR GBT_log_to_tree_remark(GBDATA *gb_tree, const char *log_entry, bool stamp)
Definition: adtree.cxx:491
NOT4PERL long * GBT_readOrCreate_int(GBDATA *gb_container, const char *fieldpath, long default_value)
Definition: adtools.cxx:402
NOT4PERL GB_ERROR GBT_remote_action_with_timeout(GBDATA *gb_main, const char *application, const char *action_name, const class ARB_timeout *timeout, bool verbose)
Definition: adtools.cxx:792
long GBT_get_alignment_len(GBDATA *gb_main, const char *aliname)
Definition: adali.cxx:706
static char * alignment_name
const char * GBT_existing_tree(GBDATA *gb_main, const char *tree_name)
Definition: adtree.cxx:1010
int GBT_is_partial(GBDATA *gb_species, int default_value, bool define_if_undef)
Definition: adali.cxx:634
GBDATA * GBT_expect_SAI(GBDATA *gb_main, const char *name)
Definition: aditem.cxx:184
GBDATA * GBT_get_tree_data(GBDATA *gb_main)
Definition: adtree.cxx:26
GB_ERROR GBT_remote_read_awar(GBDATA *gb_main, const char *application, const char *awar_name)
Definition: adtools.cxx:834
GB_ERROR GBT_add_new_changekey(GBDATA *gb_main, const char *name, int type)
bool GBT_is_alignment_protein(GBDATA *gb_main, const char *alignment_name)
Definition: adali.cxx:757
GB_ERROR(* species_callback)(GBDATA *gb_species, int *clientdata)
Definition: arbdbt.h:82
GB_ERROR GBT_link_tree(TreeNode *tree, GBDATA *gb_main, bool show_status, int *zombies, int *duplicates)
Definition: adtree.cxx:907
char * GBT_get_alignment_type_string(GBDATA *gb_main, const char *aliname)
Definition: adali.cxx:727
FILE * seq
Definition: rns.c:46
GBDATA * GBT_open(const char *path, const char *opent)
Definition: adtools.cxx:524
#define NOT4PERL
Definition: arbdb_base.h:23
char * GBT_get_default_helix_nr(GBDATA *)
Definition: adtools.cxx:65
void GBT_install_message_handler(GBDATA *gb_main)
Definition: adtools.cxx:223
GBDATA * GBT_first_species_rel_species_data(GBDATA *gb_species_data)
Definition: aditem.cxx:121
const char * GBT_get_tree_name(GBDATA *gb_tree)
Definition: adtree.cxx:1033
POS_TREE1 * father
Definition: probe_tree.h:39
NOT4PERL float * GBT_read_float(GBDATA *gb_container, const char *fieldpath)
Definition: adtools.cxx:349
GB_ERROR GBT_write_tree_remark(GBDATA *gb_main, const char *tree_name, const char *remark)
Definition: adtree.cxx:487
static FullNameMap names
GBDATA * GBT_find_SAI(GBDATA *gb_main, const char *name)
Definition: aditem.cxx:177
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()")
Definition: adali.cxx:559
GB_ERROR GBT_convert_changekey(GBDATA *gb_main, const char *name, GB_TYPES target_type)
boolean verbose
Definition: readseq.c:457
NOT4PERL long * GBT_read_int(GBDATA *gb_container, const char *fieldpath)
Definition: adtools.cxx:327
GBDATA * GBT_create_alignment(GBDATA *gbd, const char *name, long len, long aligned, long security, const char *type)
Definition: adali.cxx:387
char * GBT_read_string(GBDATA *gb_container, const char *fieldpath)
Definition: adtools.cxx:267
GB_ERROR GBT_overwrite_tree(GBDATA *gb_tree, TreeNode *tree)
Definition: adtree.cxx:480
GBT_ORDER_MODE
Definition: arbdbt.h:43
NOT4PERL void GBT_reverseComplementNucSequence(char *seq, long length, char T_or_U)
Definition: adRevCompl.cxx:102
GB_ERROR GBT_check_tree_name(const char *tree_name)
Definition: adtree.cxx:1039
void GBT_mark_all_that(GBDATA *gb_main, int flag, bool(*condition)(GBDATA *, void *), void *cd)
Definition: aditem.cxx:323
GBDATA * GBT_find_next_tree(GBDATA *gb_tree)
Definition: adtree.cxx:1017
const char * GBT_tree_info_string(GBDATA *gb_main, const char *tree_name, int maxTreeNameLen)
Definition: adtree.cxx:1068
GBDATA * gb_species_data
Definition: adname.cxx:34
GB_ERROR GBT_begin_rename_session(GBDATA *gb_main, int all_flag)
Definition: adname.cxx:42
GBDATA * GBT_find_top_tree(GBDATA *gb_main)
Definition: adtree.cxx:996
GB_ERROR GBT_set_default_alignment(GBDATA *gb_main, const char *alignment_name)
Definition: adali.cxx:680
GB_ERROR GBT_write_tree(GBDATA *gb_main, const char *tree_name, TreeNode *tree)
Definition: adtree.cxx:477
int all_flag
Definition: adname.cxx:35
GB_ERROR GBT_add_new_gene_changekey(GBDATA *gb_main, const char *name, int type)
GB_ERROR GBT_write_group_name(GBDATA *gb_group_name, const char *new_group_name, bool pedantic)
Definition: adtree.cxx:229
GBDATA * GBT_expect_species(GBDATA *gb_main, const char *name)
Definition: aditem.cxx:146
char * GBT_create_unique_species_name(GBDATA *gb_main, const char *default_name)
Definition: aditem.cxx:287
static char const * macro_name
Definition: mkptypes.cxx:81
GB_ERROR GBT_set_alignment_len(GBDATA *gb_main, const char *aliname, long new_len)
Definition: adali.cxx:714
#define __ATTR__DEPRECATED_TODO(reason)
Definition: attributes.h:104
GB_ERROR GBT_write_float_converted(GBDATA *gb_float_writable, const char *data)
char * GBT_readOrCreate_string(GBDATA *gb_container, const char *fieldpath, const char *default_value)
Definition: adtools.cxx:371
GBDATA * GBT_find_or_create_species_rel_species_data(GBDATA *gb_species_data, const char *name, bool markCreated)
Definition: aditem.cxx:57
GBDATA * GBT_next_marked_species(GBDATA *gb_species)
Definition: aditem.cxx:116
GB_ERROR GBT_copy_tree(GBDATA *gb_main, const char *source_name, const char *dest_name)
Definition: adtree.cxx:1251
void GBT_scan_db(StrArray &fieldNames, GBDATA *gbd, const char *datapath)
Definition: adtools.cxx:162
GB_ERROR GBT_rename_tree(GBDATA *gb_main, const char *source_name, const char *dest_name)
Definition: adtree.cxx:1269
TreeNode * GBT_read_tree_and_size(GBDATA *gb_main, const char *tree_name, TreeRoot *troot, int *tree_size)
Definition: adtree.cxx:724
GBDATA * GBT_first_SAI_rel_SAI_data(GBDATA *gb_sai_data)
Definition: aditem.cxx:159
GB_alignment_type GBT_get_alignment_type(GBDATA *gb_main, const char *aliname)
Definition: adali.cxx:740
const char * GBT_relativeMacroname(const char *macro_name)
Definition: adtools.cxx:907
GBDATA * GBT_find_species_rel_species_data(GBDATA *gb_species_data, const char *name)
Definition: aditem.cxx:133
long GBT_size_of_tree(GBDATA *gb_main, const char *tree_name)
Definition: adtree.cxx:1111
NewickFormat
Definition: arbdb_base.h:68
GB_ERROR GBT_remote_action(GBDATA *gb_main, const char *application, const char *action_name)
Definition: adtools.cxx:809
char * GBT_get_default_ref(GBDATA *)
Definition: adtools.cxx:66
GB_TYPES GBT_get_type_of_changekey(GBDATA *gb_main, const char *field_name, const char *change_key_path)
Definition: adChangeKey.cxx:34
NOT4PERL float * GBT_readOrCreate_float(GBDATA *gb_container, const char *fieldpath, float default_value)
Definition: adtools.cxx:422
GBDATA * GBT_find_sequence(GBDATA *gb_species, const char *aliname)
Definition: adali.cxx:670
char * GBT_read_gene_sequence(GBDATA *gb_gene, bool use_revComplement, char partSeparator)
Definition: adali.cxx:919
GB_ERROR GBT_abort_rename_session(void)
Definition: adname.cxx:130
GB_ERROR GBT_commit_rename_session(void) __ATTR__USERESULT
Definition: adname.cxx:169
long GBT_count_marked_species(GBDATA *gb_main)
Definition: aditem.cxx:353
const char * GBT_readOrCreate_char_pntr(GBDATA *gb_container, const char *fieldpath, const char *default_value)
Definition: adtools.cxx:386
GB_alignment_type
Definition: arbdb_base.h:61
long int flag
Definition: f2c.h:39
GB_ERROR GBT_write_byte(GBDATA *gb_container, const char *fieldpath, unsigned char content)
Definition: adtools.cxx:486
GBDATA * GBT_searchOrCreate_itemfield_according_to_changekey(GBDATA *gb_item, const char *field_name, const char *change_key_path)
Definition: adChangeKey.cxx:62
GBDATA * GBT_next_SAI(GBDATA *gb_sai)
Definition: aditem.cxx:166
static void copy(double **i, double **j)
Definition: trnsprob.cxx:32
GB_ERROR GBT_remote_awar(GBDATA *gb_main, const char *application, const char *awar_name, const char *value)
Definition: adtools.cxx:815
GB_CSTR GBT_read_name(GBDATA *gb_item) __ATTR__DEPRECATED_TODO("please use GBT_get_name or GBT_get_name_or_description()")
Definition: aditem.cxx:459
GB_ERROR GBT_is_invalid(const TreeNode *tree)
Definition: adtree.cxx:834
GB_ERROR GBT_write_string(GBDATA *gb_container, const char *fieldpath, const char *content)
Definition: adtools.cxx:451
GBDATA * GBT_get_changekey(GBDATA *gb_main, const char *key, const char *change_key_path)
Definition: adChangeKey.cxx:16
#define __ATTR__USERESULT
Definition: attributes.h:58
GB_ERROR GBT_write_float(GBDATA *gb_container, const char *fieldpath, float content)
Definition: adtools.cxx:502
GBDATA * GBT_create(GBDATA *father, const char *key, long delete_level)
Definition: adtools.cxx:26
GBDATA * GBT_find_or_create(GBDATA *father, const char *key, long delete_level)
Definition: adtools.cxx:42
GBDATA * GBT_gen_accession_number(GBDATA *gb_species, const char *ali_name)
Definition: adali.cxx:617
GBDATA * GBT_first_species(GBDATA *gb_main)
Definition: aditem.cxx:124
char * GBT_read_as_string(GBDATA *gb_container, const char *fieldpath)
Definition: adtools.cxx:290
void GBT_get_tree_names(ConstStrArray &names, GBDATA *gb_main, bool sorted)
Definition: adtree.cxx:1136
void GBT_message(GBDATA *gb_main, const char *msg)
Definition: adtools.cxx:238
GB_ERROR GBT_compress_sequence_tree2(GBDATA *gbd, const char *tree_name, const char *ali_name) __ATTR__USERESULT
Definition: adseqcompr.cxx:889
GB_ERROR GBT_add_new_changekey_to_keypath(GBDATA *gb_main, const char *name, int type, const char *keypath)
Definition: adChangeKey.cxx:87
char * GBT_get_default_helix(GBDATA *)
Definition: adtools.cxx:64
GB_ERROR GB_clear_macro_error(GBDATA *gb_main)
Definition: adtools.cxx:699
GBDATA * GBT_find_or_create_species(GBDATA *gb_main, const char *name, bool markCreated)
Definition: aditem.cxx:61
GBDATA * GBT_next_species(GBDATA *gb_species)
Definition: aditem.cxx:128
GB_ERROR GBT_write_name_to_groupData(GBDATA *gb_group, bool createNameEntry, const char *new_group_name, bool pedantic)
Definition: adtree.cxx:279
GBDATA * GBT_find_species(GBDATA *gb_main, const char *name)
Definition: aditem.cxx:139
GB_CSTR * GBT_get_names_of_species_in_tree(const TreeNode *tree, size_t *count)
Definition: adtree.cxx:1291
NOT4PERL GBDATA * GBT_create_sequence_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type, int security_write)
Definition: adali.cxx:605
char * GBT_get_default_alignment(GBDATA *gb_main)
Definition: adali.cxx:675
const char * GBT_get_name(GBDATA *gb_item)
Definition: aditem.cxx:450
GBDATA * GBT_find_SAI_rel_SAI_data(GBDATA *gb_sai_data, const char *name)
Definition: aditem.cxx:171
GB_TYPES
Definition: arbdb.h:62
void GBT_mark_all(GBDATA *gb_main, int flag)
Definition: aditem.cxx:295
char * GBT_store_marked_species(GBDATA *gb_main, bool unmark_all)
Definition: aditem.cxx:358
GBDATA * GBT_find_or_create_SAI(GBDATA *gb_main, const char *name)
Definition: aditem.cxx:65
long GBT_get_species_count(GBDATA *gb_main)
Definition: aditem.cxx:207
GBDATA * GBT_find_item_rel_item_data(GBDATA *gb_item_data, const char *id_field, const char *id_value)
Definition: aditem.cxx:74
GB_ERROR GBT_add_new_experiment_changekey(GBDATA *gb_main, const char *name, int type)
GBDATA * GBT_find_tree(GBDATA *gb_main, const char *tree_name)
Definition: adtree.cxx:947
GB_ERROR GBT_write_int(GBDATA *gb_container, const char *fieldpath, long content)
Definition: adtools.cxx:471
GBDATA * gb_main
Definition: adname.cxx:33
NOT4PERL char * GBT_read_gene_sequence_and_length(GBDATA *gb_gene, bool use_revComplement, char partSeparator, size_t *gene_length)
Definition: adali.cxx:817
GB_ERROR GBT_check_data(GBDATA *Main, const char *alignment_name)
Definition: adali.cxx:217
GBDATA * GBT_get_presets(GBDATA *gb_main)
Definition: adali.cxx:29
GBDATA * GBT_get_SAI_data(GBDATA *gb_main)
Definition: aditem.cxx:154
GB_CSTR GBT_get_name_or_description(GBDATA *gb_item)
Definition: aditem.cxx:441
size_t length
GB_ERROR GBT_write_int_converted(GBDATA *gb_int_writable, const char *data, size_t *rounded)
GB_ERROR GB_get_macro_error(GBDATA *gb_main)
Definition: adtools.cxx:687
const char * GBT_read_char_pntr(GBDATA *gb_container, const char *fieldpath)
Definition: adtools.cxx:307
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)
Definition: aditem.cxx:18
const char * GB_CSTR
Definition: arbdb_base.h:25
static const char * action_name[]
Definition: AWTI_edit.cxx:37
GBDATA * GBT_tree_infrontof(GBDATA *gb_tree)
Definition: adtree.cxx:985
NOT4PERL GB_ERROR GBT_determine_T_or_U(GB_alignment_type alignment_type, char *T_or_U, const char *supposed_target)
Definition: adRevCompl.cxx:90
GB_ERROR GBT_rename_alignment(GBDATA *gbMain, const char *source, const char *dest, int copy, int dele)
Definition: adali.cxx:481
GBDATA * GBT_get_species_data(GBDATA *gb_main)
Definition: aditem.cxx:105
GB_write_int const char s
Definition: AW_awar.cxx:156