ARB
Macros | Typedefs | Enumerations | Functions
arbdbt.h File Reference
#include <arbdb.h>
#include <downcast.h>
#include <ad_t_prot.h>
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Macros

#define gb_assert(cond)   arb_assert(cond)
 
#define GBT_SPECIES_INDEX_SIZE   10000L
 
#define GBT_SAI_INDEX_SIZE   1000L
 
#define GB_GROUP_NAME_MAX   256
 
#define DEFAULT_BRANCH_LENGTH   0.1
 
#define ERROR_CONTAINER_PATH   "tmp/message/pending"
 
#define REMOTE_BASE   "tmp/remote/"
 
#define MACRO_TRIGGER_CONTAINER   REMOTE_BASE "trigger"
 
#define MACRO_TRIGGER_TERMINATED   MACRO_TRIGGER_CONTAINER "/terminated"
 
#define MACRO_TRIGGER_RECORDING   MACRO_TRIGGER_CONTAINER "/recording"
 
#define MACRO_TRIGGER_ERROR   MACRO_TRIGGER_CONTAINER "/error"
 
#define MACRO_TRIGGER_TRACKED   MACRO_TRIGGER_CONTAINER "/tracked"
 
#define SRT_AUTOCORRECT_TREENAME   " =:\n=:*=tree_*1:tree_tree_*=tree_*1"
 
#define SRT_AUTOCORRECT_ALINAME   " =:\n=:*=ali_*1:ali_ali_*=ali_*1"
 
#define CHANGE_KEY_PATH   "presets/key_data"
 
#define CHANGE_KEY_PATH_GENES   "presets/gene_key_data"
 
#define CHANGE_KEY_PATH_EXPERIMENTS   "presets/experiment_key_data"
 
#define CHANGEKEY   "key"
 
#define CHANGEKEY_NAME   "key_name"
 
#define CHANGEKEY_TYPE   "key_type"
 
#define CHANGEKEY_HIDDEN   "key_hidden"
 

Typedefs

typedef GB_ERROR(* species_callback )(GBDATA *gb_species, int *clientdata)
 

Enumerations

enum  GBT_RemarkType { REMARK_NONE, REMARK_BOOTSTRAP, REMARK_OTHER }
 
enum  GBT_TreeRemoveType { GBT_REMOVE_MARKED = 1, GBT_REMOVE_UNMARKED = 2, GBT_REMOVE_ZOMBIES = 4, GBT_KEEP_MARKED = GBT_REMOVE_UNMARKED|GBT_REMOVE_ZOMBIES }
 
enum  GBT_ORDER_MODE { GBT_BEHIND, GBT_INFRONTOF }
 
enum  TreeModel { ROOTED = 0, UNROOTED = 1 }
 

Functions

CONSTEXPR_INLINE int nodes_2_edges (int nodes)
 
CONSTEXPR_INLINE int edges_2_nodes (int nodes)
 
CONSTEXPR_INLINE int leafs_2_nodes (int leafs, TreeModel model)
 
CONSTEXPR_INLINE int nodes_2_leafs (int nodes, TreeModel model)
 
CONSTEXPR_INLINE int leafs_2_edges (int leafs, TreeModel model)
 
CONSTEXPR_INLINE int edges_2_leafs (int edges, TreeModel model)
 
CONSTEXPR_INLINE int leafs_2_innerNodes (int leafs, TreeModel model)
 
CONSTEXPR_INLINE int nodes_2_innerNodes (int nodes, TreeModel model)
 

Macro Definition Documentation

#define gb_assert (   cond)    arb_assert(cond)

Definition at line 11 of file arbdbt.h.

Referenced by CallbackList< gb_callback >::add(), add_dtree_to_dtree(), add_to_dtree(), GBENTRY::alloc_data(), ALPHA_DICT_OFFSET(), gb_local_data::announce_db_close(), gb_local_data::announce_db_open(), TreeNode::announce_tree_constructed(), apply_filters(), ARBDB_memory_manager::ARBDB_memory_manager(), GBDATA::as_container(), GBDATA::as_entry(), build_dict_tree(), build_taxonomy_rek(), buildAllowedValuesString(), cache_free_some_memory(), calcCounts(), gb_pending_callbacks::call_and_forget(), cbtype2readable(), GBL_IMPL::check_has_parameters(), GBL_IMPL::check_no_parameter(), GBL_IMPL::check_optional_parameters(), GBL_IMPL::check_parameters(), clear_comment_cb(), GB_MAIN_TYPE::commit_transaction(), TextRef::compare(), compress_sequence_tree(), convert_case(), convertFlags4Save(), copy_tree_container(), count_dtree_leafs(), distribute_masters(), downheap(), downheap2(), dummy_db_cb(), ensure_trees_have_order(), EXP_next_experiment(), expandBranches(), filter_seq(), find_gbdata_offset(), find_or_create(), find_sub_by_quark(), ArbDBWriter::finishSave(), TreeNode::fixDeletedSon(), flush_cache_entry(), format(), ftwrite_aligned(), fullMacroname(), g_b_Consensus_add(), g_b_opti_scanGbdByKey(), g_b_put_number2(), g_b_read_number2(), g_b_uncompress_single_sequence_by_master(), gb_abortdata(), gb_add_callback(), gb_alloc_cache_index(), gb_callback::gb_callback(), GB_canonical_path(), GB_check_hkey(), GB_clear_user_flag(), GB_clone(), gb_clone_explicit(), GB_close(), GB_command_interpreter_in_env(), gb_compress_by_dictionary(), gb_compress_data(), gb_compress_huffmann(), GB_concat_full_path(), gb_convert_compression(), gb_copy_explicit(), gb_create(), GB_create(), GB_create_container(), gb_create_dictionaries(), gb_create_dictionary(), gb_create_header_array(), gb_create_key(), gb_create_key_array(), gb_delete_dummy_father(), gb_delete_entry(), gb_do_callbacks(), GB_existing_file(), gb_expect_type(), gb_find_internal(), gb_find_value_equal(), gb_fix_recursive(), GB_get_subfields(), GB_get_supported_compression_flags(), GB_get_usable_memory(), GB_getenvARB_XCMD(), GB_getenvHOME(), gb_hierarchy_location::gb_hierarchy_location(), GB_inside_callback(), GB_inside_remote_action(), GB_install_pid(), GB_log_fak(), GB_login(), gb_make_main_idx(), gb_map_mapfile(), gb_parse_ascii_rek(), GB_raise_user_flag(), GB_read_as_string(), gb_read_bin(), gb_read_bin_rek_V2(), gb_read_cache(), GB_read_float(), GB_read_lossless_byte(), GB_read_lossless_float(), GB_read_lossless_int(), gb_remove_callbacks_that(), GB_save_as(), gb_save_mapfile(), gb_search(), GB_searchOrCreate_float(), GB_searchOrCreate_int(), GB_searchOrCreate_string(), GB_set_export_sequence_hook(), GB_set_remote_action(), GB_split_full_path(), GB_start_streamed_save_as(), gb_transactable_type(), gb_uncompress_by_dictionary_internal(), gb_uncompress_by_sequence(), gb_uncompress_bytes(), gb_uncompress_equal_bytes(), gb_uncompress_huffmann(), gb_uncompress_longs_old(), GB_unfold_path(), GB_user_flag(), gb_write_bin(), gb_write_bin_rek(), gb_write_bin_sub_containers(), gb_write_childs(), gb_write_compressed_pntr(), GB_write_float(), GB_write_int(), GB_write_lossless_float(), GB_write_lossless_int(), gb_write_one_child(), GB_write_pntr(), GB_write_string(), GB_xcmd(), gbcm_logout(), GBCMC_find(), gbcmc_key_alloc(), gbcms_talking_find(), gbl_apply_binary_operator(), GBL_command_lookup_table::GBL_command_lookup_table(), gbl_crop(), gbl_exec(), gbl_export_sequence(), gbl_extract_sequence(), gbl_extract_words(), gbl_mid_streams(), gbl_read_seq_sai_or_species(), gbl_stristr(), gbl_swap(), gbl_taxonomy(), gbm_flush_mem(), gbm_get_memblk(), gbm_put_memblk(), GBS_erase_hash(), GBS_escape_string(), GBS_fconvert_string(), GBS_free_hash(), gbs_get_a_prime(), GBS_ptserver_tag(), GBS_read_arb_tcp(), GBS_read_dir(), gbs_scan_db_insert(), GBS_shorten_repeated_data(), GBS_string_eval_in_env(), GBS_string_matches_regexp(), GBS_unescape_string(), GBS_write_numhash(), GBT_add_new_changekey_to_keypath(), GBT_append_to_config_string(), GBT_check_alignment(), GBT_check_arb_file(), GBT_create(), GBT_create_alignment(), GBT_create_unique_item_identifier(), GBT_find_next_tree(), GBT_find_or_create(), GBT_get_alignment_type(), GBT_get_alignment_type_string(), GBT_get_default_alignment(), GBT_get_names_of_species_in_tree(), GBT_get_tree_name(), GBT_get_tree_names(), GBT_install_message_handler(), GBT_mark_all(), GBT_mark_all_that(), GBT_message(), GBT_move_tree(), GBT_next_marked_species(), GBT_next_SAI(), GBT_next_species(), GBT_open(), GBT_read_gene_sequence_and_length(), GBT_read_tree_and_size(), gbt_read_tree_rek(), GBT_readOrCreate_float(), GBT_remove_leafs(), GBT_rename_alignment(), GBT_rename_species(), gbt_scan_db_rek(), gbt_scan_db_start(), GBT_searchOrCreate_itemfield_according_to_changekey(), GBT_tree_2_newick(), GBT_with_stored_species(), GBT_write_byte(), GBT_write_float(), GBT_write_group_name(), GBT_write_int(), GBT_write_string(), gbt_write_tree(), gbt_write_tree_rek_new(), GEN_add_pseudo_species_to_hash(), GEN_create_nonexisting_gene_rel_gene_data(), GEN_expect_gene_data(), GEN_find_origin_gene(), GEN_find_origin_organism(), GEN_findOrCreate_gene_data(), GEN_global_gene_identifier(), GEN_is_organism(), GEN_new_position(), GEN_next_gene(), GEN_organism_not_found(), GEN_read_position(), GEN_write_position(), get_cached_taxonomy(), get_data_n_size(), FINAL_TYPE< SEQTYPE >::get_leaf_count(), get_next_tree(), ArbTcpDat::get_serverID(), get_source_and_check_target_tree(), FINAL_TYPE< SEQTYPE >::get_target_data(), get_taxonomy_string(), get_tree_behind_idx(), get_tree_idx(), get_tree_infrontof_idx(), getClusterIndex(), getPartPositions(), getrel_GBDATA(), TextRef::icompare(), INDEX_DICT_OFFSET(), GBENTRY::insert_data(), TreeNode::is_leftson(), TextRef::is_part_of(), TreeNode::is_rightson(), gb_hierarchy_location::is_submatch(), link_cache_entry_to_top(), MAKEREL(), mark_as_macro_executor(), gb_hierarchy_location::matches(), GBL_IMPL::modify_trace_indent(), GBT_config_parser::nextItem(), TypedDatabaseCallback::operator()(), TextRef::partBefore(), TextRef::partBehind(), GBL_IMPL::print_trace(), protect_corruption_error(), read_keyword(), read_tree_and_size_internal(), readAndWrite(), GB_MAIN_TYPE::release_main_idx(), remove_word_from_dtree(), removeSubsequentString(), renameQuicksaves(), run_close_callbacks(), GB_MAIN_TYPE::save_quick(), ArbDBWriter::saveFromTill(), scanGbdByKey(), searchWord(), TreeNode::set_branchlength(), set_masters_with_sons(), set_protection_level(), shortenLongString(), single2full_dtree(), sort_gbdata_offsets(), start_remote_command_for_application(), ArbDBWriter::startSaveAs(), STATIC_BUFFER(), string2enum(), TreeNode::swap_node_info(), GBL_IMPL::trace_params(), tree2newick(), GB_MAIN_TYPE::trigger_delete_callbacks(), GBDATA::type(), unlink_cache_entry(), write_GBDATA(), writeGbdByKey(), ArbDBWriter::~ArbDBWriter(), BufferedPipeReader::~BufferedPipeReader(), gb_cache::~gb_cache(), gb_local_data::~gb_local_data(), GB_MAIN_TYPE::~GB_MAIN_TYPE(), GB_shell::~GB_shell(), GB_transaction::~GB_transaction(), and TreeNode::~TreeNode().

#define GBT_SPECIES_INDEX_SIZE   10000L

Definition at line 13 of file arbdbt.h.

Referenced by GBT_open().

#define GBT_SAI_INDEX_SIZE   1000L

Definition at line 14 of file arbdbt.h.

Referenced by GBT_open().

#define GB_GROUP_NAME_MAX   256

Definition at line 16 of file arbdbt.h.

Referenced by GBT_write_group_name(), group_species(), and EDB_root_bact::scan_string().

#define DEFAULT_BRANCH_LENGTH   0.1
#define ERROR_CONTAINER_PATH   "tmp/message/pending"

Definition at line 20 of file arbdbt.h.

Referenced by find_or_create_error_container().

#define REMOTE_BASE   "tmp/remote/"

Definition at line 22 of file arbdbt.h.

Referenced by getKnownMacroClients().

#define MACRO_TRIGGER_CONTAINER   REMOTE_BASE "trigger"

Definition at line 23 of file arbdbt.h.

Referenced by getKnownMacroClients().

#define MACRO_TRIGGER_TERMINATED   MACRO_TRIGGER_CONTAINER "/terminated"

Definition at line 24 of file arbdbt.h.

Referenced by MacroRecorder::execute(), and mark_as_macro_executor().

#define MACRO_TRIGGER_RECORDING   MACRO_TRIGGER_CONTAINER "/recording"

Definition at line 25 of file arbdbt.h.

Referenced by announce_recording(), and create_macro_variables().

#define MACRO_TRIGGER_ERROR   MACRO_TRIGGER_CONTAINER "/error"

Definition at line 26 of file arbdbt.h.

Referenced by GB_clear_macro_error(), GB_get_macro_error(), and GB_set_macro_error().

#define MACRO_TRIGGER_TRACKED   MACRO_TRIGGER_CONTAINER "/tracked"

Definition at line 27 of file arbdbt.h.

Referenced by check_for_remote_command().

#define SRT_AUTOCORRECT_TREENAME   " =:\n=:*=tree_*1:tree_tree_*=tree_*1"

Definition at line 79 of file arbdbt.h.

Referenced by TreeAdmin::create_awars(), and create_trees_var().

#define SRT_AUTOCORRECT_ALINAME   " =:\n=:*=ali_*1:ali_ali_*=ali_*1"
#define CHANGE_KEY_PATH   "presets/key_data"
#define CHANGE_KEY_PATH_GENES   "presets/gene_key_data"
#define CHANGE_KEY_PATH_EXPERIMENTS   "presets/experiment_key_data"
#define CHANGEKEY   "key"
#define CHANGEKEY_NAME   "key_name"
#define CHANGEKEY_TYPE   "key_type"
#define CHANGEKEY_HIDDEN   "key_hidden"

Typedef Documentation

typedef GB_ERROR(* species_callback)(GBDATA *gb_species, int *clientdata)

Definition at line 82 of file arbdbt.h.

Enumeration Type Documentation

Enumerator
REMARK_NONE 
REMARK_BOOTSTRAP 
REMARK_OTHER 

Definition at line 29 of file arbdbt.h.

Enumerator
GBT_REMOVE_MARKED 
GBT_REMOVE_UNMARKED 
GBT_REMOVE_ZOMBIES 
GBT_KEEP_MARKED 

Definition at line 31 of file arbdbt.h.

Enumerator
GBT_BEHIND 
GBT_INFRONTOF 

Definition at line 43 of file arbdbt.h.

enum TreeModel
Enumerator
ROOTED 
UNROOTED 

Definition at line 48 of file arbdbt.h.

Function Documentation

CONSTEXPR_INLINE int nodes_2_edges ( int  nodes)

Definition at line 50 of file arbdbt.h.

Referenced by LongBranchMarker::get_report(), and leafs_2_edges().

CONSTEXPR_INLINE int edges_2_nodes ( int  nodes)

Definition at line 51 of file arbdbt.h.

Referenced by edges_2_leafs().

CONSTEXPR_INLINE int leafs_2_nodes ( int  leafs,
TreeModel  model 
)

calculate the number of (leaf- plus inner-)nodes in a tree with 'leafs' leafs

Definition at line 53 of file arbdbt.h.

Referenced by freeTree(), LongBranchMarker::get_report(), ConsensusTree::insert_tree_weighted(), leafs_2_edges(), leafs_2_innerNodes(), NTREE_move_tree_info(), AP_pos_var::retrieve(), and setuptree().

CONSTEXPR_INLINE int nodes_2_leafs ( int  nodes,
TreeModel  model 
)

calculate the number of leafs in a tree with 'nodes' (leaf- plus inner-)nodes

Definition at line 57 of file arbdbt.h.

Referenced by edges_2_leafs(), and nodes_2_innerNodes().

CONSTEXPR_INLINE int leafs_2_edges ( int  leafs,
TreeModel  model 
)

calculate the number of edges in a tree with 'leafs' leafs

Definition at line 61 of file arbdbt.h.

References leafs_2_nodes(), and nodes_2_edges().

Referenced by calc_steps(), ARB_edge::iteration_count(), and PartRegistry::put_part_from_partial_tree().

CONSTEXPR_INLINE int edges_2_leafs ( int  edges,
TreeModel  model 
)

calculate the number of leafs in a tree with 'edges' edges

Definition at line 65 of file arbdbt.h.

References edges_2_nodes(), and nodes_2_leafs().

CONSTEXPR_INLINE int leafs_2_innerNodes ( int  leafs,
TreeModel  model 
)

calculate the number of inner nodes in a tree with 'leafs' leafs

Definition at line 70 of file arbdbt.h.

References leafs_2_nodes().

CONSTEXPR_INLINE int nodes_2_innerNodes ( int  nodes,
TreeModel  model 
)

calculate the number of inner nodes in a tree with 'nodes' (leaf- plus inner-)nodes

Definition at line 74 of file arbdbt.h.

References nodes_2_leafs().